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(-) Description

Title :  CRYSTAL STRUCTURE OF SMALL PROTEIN CRAMBIN AT 0.48 A RESOLUTION
 
Authors :  A. Schmidt, M. Teeter, E. Weckert, V. S. Lamzin
Date :  16 Jun 10  (Deposition) - 18 May 11  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.48
Chains :  Asym./Biol. Unit :  A
Keywords :  Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Schmidt, M. Teeter, E. Weckert, V. S. Lamzin
Crystal Structure Of Small Protein Crambin At 0. 48 A Resolution
Acta Crystallogr. , Sect. F V. 67 424 2011
PubMed-ID: 21505232
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CRAMBIN
    Chains: A
    Organism Common: ABYSSINIAN CRAMBE, ABYSSINIAN KALE
    Organism Scientific: CRAMBE HISPANICA
    Organism Taxid: 3721
    Strain: SUBSP. ABYSSINICA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1EOH4Ligand/IonETHANOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:45 , ASN A:46 , EOH A:2004 , HOH A:3006 , HOH A:3027 , HOH A:3038 , HOH A:3087 , HOH A:3091BINDING SITE FOR RESIDUE EOH A 2001
2AC2SOFTWAREILE A:7 , VAL A:8 , SER A:11 , ALA A:27 , GLY A:31 , CYS A:32 , ILE A:33 , HOH A:3002 , HOH A:3068 , HOH A:3102BINDING SITE FOR RESIDUE EOH A 2002
3AC3SOFTWAREILE A:7 , ASN A:46 , HOH A:3063BINDING SITE FOR RESIDUE EOH A 2003
4AC4SOFTWAREASN A:14 , LEU A:18 , EOH A:2001 , HOH A:3011 , HOH A:3020 , HOH A:3023 , HOH A:3085BINDING SITE FOR RESIDUE EOH A 2004

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:40
2A:4 -A:32
3A:16 -A:26

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NIR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CRAM_CRAAB_001 *P22SCRAM_CRAAB  ---  ---AP22S
2UniProtVAR_CRAM_CRAAB_002 *L25ICRAM_CRAAB  ---  ---AL25I
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIONINPS00271 Plant thionins signature.CRAM_CRAAB3-16  1A:3-16

(-) Exons   (0, 0)

(no "Exon" information available for 3NIR)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
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:48
 aligned with CRAM_CRAAB | P01542 from UniProtKB/Swiss-Prot  Length:46

    Alignment length:48
                                                      26                    
                                                    25 |                    
                                                  23 | |                    
                                                22 | | |                    
                                    10        20 | | | |28        38        
            CRAM_CRAAB    1 TTCCPSIVARSNFNVCRLPGTP-EAL-CATYTGCIIIPGATCPGDYAN 46
               SCOP domains d3nira_ A: automated aatcees                     SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains Thionin-3nirA01 A:1-4                            Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhh................ee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE --THIONIN       -------------------------------- PROSITE
                 Transcript ------------------------------------------------ Transcript
                  3nir A  1 TTCCPSIVARSNFNVCRLPGTPSEALICATYTGCIIIPGATCPGDYAN 46
                                    10        20        28        38
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NIR)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Thionin] (10)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CRAM_CRAAB | P01542)
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CRAM_CRAAB | P01542: 1ab1 1cbn 1ccm 1ccn 1cnr 1crn 1cxr 1ejg 1jxt 1jxu 1jxw 1jxx 1jxy 1yv8 1yva 2eya 2eyb 2eyc 2eyd 2fd7 2fd9 3u7t 3ue7 4fc1

(-) Related Entries Specified in the PDB File

1ab1 CRAMBIN, PURE S22 / I25 FORM
1cbn CRAMBIN TO 0.83 A RESOLUTION
1cnr CRAMBIN, PURE P22/ L25 FORM
1crn CRAMBIN AT ROOM TEMPERATURE
1ejg CRAMBIN TO 0.54 A RESOLUTION