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(-) Description

Title :  JOINT X-RAY AND NEUTRON STRUCTURE OF STREPTOMYCES RUBIGINOSUS D-XYLOSE ISOMERASE IN COMPLEX WITH TWO CD2+ IONS AND CYCLIC BETA-L-ARABINOSE
 
Authors :  A. Y. Kovalevsky, P. Langan
Date :  14 May 14  (Deposition) - 03 Sep 14  (Release) - 10 Sep 14  (Revision)
Method :  NEUTRON DIFFRACTION; X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Tim Barrel, Sugar Isomerase, Monosaccharides, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Langan, A. K. Sangha, T. Wymore, J. M. Parks, Z. K. Yang, B. L. Hanson, Z. Fisher, S. A. Mason, M. P. Blakeley, V. T. Forsyth, J. P. Glusker, H. L. Carrell, J. C. Smith, D. A. Keen, D. E. Graham, A. Kovalevsky
L-Arabinose Binding, Isomerization, And Epimerization By D-Xylose Isomerase: X-Ray/Neutron Crystallographic And Molecular Simulation Study.
Structure V. 22 1287 2014
PubMed-ID: 25132082  |  Reference-DOI: 10.1016/J.STR.2014.07.002

(-) Compounds

Molecule 1 - XYLOSE ISOMERASE
    Chains: A
    EC Number: 5.3.1.5
    Organism Scientific: STREPTOMYCES RUBIGINOSUS
    Organism Taxid: 1929

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 315)

Asymmetric Unit (3, 315)
No.NameCountTypeFull Name
1ARB1Ligand/IonBETA-L-ARABINOSE
2CD2Ligand/IonCADMIUM ION
3DOD312Ligand/Ion
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ARB4Ligand/IonBETA-L-ARABINOSE
2CD-1Ligand/IonCADMIUM ION
3DOD-1Ligand/Ion

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:217 , HIS A:220 , ASP A:255 , ASP A:257 , DOD A:1001BINDING SITE FOR RESIDUE CD A 401
2AC2SOFTWAREGLU A:181 , GLU A:217 , ASP A:245 , ASP A:287 , ARB A:403BINDING SITE FOR RESIDUE CD A 402
3AC3SOFTWARETRP A:16 , PHE A:26 , HIS A:54 , PHE A:94 , TRP A:137 , GLU A:181 , GLU A:217 , HIS A:220 , ASP A:245 , ASP A:287 , CD A:402 , DOD A:1001 , DOD A:1095 , DOD A:1150 , DOD A:1195BINDING SITE FOR RESIDUE ARB A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QDP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:186 -Pro A:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QDP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QDP)

(-) Exons   (0, 0)

(no "Exon" information available for 4QDP)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh.eeeehhhhh...............hhhhhhhhhhhhh..eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeee.....ee......hhhhhhhhhhhhhhhhhhhhhhhh...eeee.........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhh......ee.................hhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qdp A   1 MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG 388
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4QDP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QDP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QDP)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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    Glu A:186 - Pro A:187   [ RasMol ]  
 
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  XYLA_STRRU | P24300
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        XYLA_STRRU | P24300: 1gw9 1mnz 1o1h 1oad 1xib 1xic 1xid 1xie 1xif 1xig 1xih 1xii 1xij 1xis 2g4j 2glk 2gub 2gve 2xis 3cwh 3gnx 3kbj 3kbm 3kbn 3kbs 3kbv 3kbw 3kcj 3kcl 3kco 3n4a 3qys 3qza 3u3h 3xis 4a8i 4a8l 4a8n 4a8r 4duo 4dvo 4e3v 4j4k 4lnc 4qdw 4qe1 4qe4 4qe5 4qee 4qeh 4us6 4w4q 4xis 4zb0 4zb2 4zb5 4zbc 5avh 5avn 5i7g 8xia 9xia

(-) Related Entries Specified in the PDB File

4qdw 4qe1 4qe4 4qe5 4qee 4qeh