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(-) Description

Title :  CRYSTAL STRUCTURE OF A BETAGAMMA-CRYSTALLIN DOMAIN FROM FLAVOBACTERIUM JOHNSONIAE
 
Authors :  P. Aravind, R. Sankaranarayanan
Date :  23 Jun 09  (Deposition) - 01 Dec 09  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Calcium-Bound Betagamma-Crystallin, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Aravind, A. Mishra, S. K. Suman, M. K. Jobby, R. Sankaranarayanan, Y. Sharma
The Betagamma-Crystallin Superfamily Contains A Universal Motif For Binding Calcium
Biochemistry V. 48 12180 2009
PubMed-ID: 19921810  |  Reference-DOI: 10.1021/BI9017076
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOHYDRATE BINDING PROTEIN
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 501-590
    Gene: 5093804
    Organism Common: CYTOPHAGA JOHNSONAE
    Organism Scientific: FLAVOBACTERIUM JOHNSONIAE
    Organism Taxid: 376686
    Strain: UW101
    Synonym: FLAVOLLIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 20)

Asymmetric Unit (1, 20)
No.NameCountTypeFull Name
1CA20Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:7 , ASP A:37 , SER A:39 , ASP A:77 , HOH A:93 , HOH A:94 , HOH A:97BINDING SITE FOR RESIDUE CA A 101
02AC2SOFTWAREASP A:36 , GLN A:53 , LYS A:78 , SER A:80 , HOH A:92 , HOH A:100 , HOH A:149 , HOH A:674BINDING SITE FOR RESIDUE CA A 102
03AC3SOFTWAREILE A:43 , ASP A:67 , HOH A:96 , ILE B:43 , ASP B:67 , HOH B:208BINDING SITE FOR RESIDUE CA A 117
04AC4SOFTWARELYS B:7 , ASP B:37 , SER B:39 , ASP B:77 , HOH B:91 , HOH B:94 , HOH B:212BINDING SITE FOR RESIDUE CA B 107
05AC5SOFTWAREASP B:36 , GLN B:53 , LYS B:78 , SER B:80 , HOH B:97 , HOH B:100 , HOH B:163 , HOH B:181BINDING SITE FOR RESIDUE CA B 108
06AC6SOFTWARELYS C:7 , ASP C:37 , SER C:39 , ASP C:77 , HOH C:94 , HOH C:95 , HOH C:98BINDING SITE FOR RESIDUE CA C 103
07AC7SOFTWAREASP C:36 , GLN C:53 , LYS C:78 , SER C:80 , HOH C:100 , HOH C:109 , HOH C:137 , HOH C:318BINDING SITE FOR RESIDUE CA C 104
08AC8SOFTWAREILE C:43 , ASP C:67 , HOH C:101 , ILE D:43 , ASP D:67 , HOH D:98BINDING SITE FOR RESIDUE CA C 118
09AC9SOFTWARELYS D:7 , ASP D:37 , SER D:39 , ASP D:77 , HOH D:94 , HOH D:96 , HOH D:191BINDING SITE FOR RESIDUE CA D 105
10BC1SOFTWAREASP D:36 , GLN D:53 , LYS D:78 , SER D:80 , HOH D:99 , HOH D:101 , HOH D:103 , HOH D:375BINDING SITE FOR RESIDUE CA D 106
11BC2SOFTWARELYS E:7 , ASP E:37 , SER E:39 , ASP E:77 , HOH E:93 , HOH E:104 , HOH E:235BINDING SITE FOR RESIDUE CA E 109
12BC3SOFTWAREASP E:36 , GLN E:53 , LYS E:78 , SER E:80 , HOH E:97 , HOH E:101 , HOH E:105 , HOH E:441BINDING SITE FOR RESIDUE CA E 110
13BC4SOFTWAREILE E:43 , ASP E:67 , HOH E:106 , ILE F:43 , ASP F:67 , HOH F:115BINDING SITE FOR RESIDUE CA E 119
14BC5SOFTWARELYS F:7 , ASP F:37 , SER F:39 , ASP F:77 , HOH F:93 , HOH F:95 , HOH F:96BINDING SITE FOR RESIDUE CA F 113
15BC6SOFTWAREASP F:36 , GLN F:53 , LYS F:78 , SER F:80 , HOH F:102 , HOH F:109 , HOH F:141 , HOH F:474BINDING SITE FOR RESIDUE CA F 114
16BC7SOFTWARELYS G:7 , ASP G:37 , SER G:39 , ASP G:77 , HOH G:92 , HOH G:206 , HOH G:672BINDING SITE FOR RESIDUE CA G 111
17BC8SOFTWAREASP G:36 , GLN G:53 , LYS G:78 , SER G:80 , HOH G:95 , HOH G:97 , HOH G:151 , HOH G:157BINDING SITE FOR RESIDUE CA G 112
18BC9SOFTWAREILE G:43 , ASP G:67 , HOH G:249 , ILE H:43 , ASP H:67 , HOH H:93BINDING SITE FOR RESIDUE CA G 120
19CC1SOFTWARELYS H:7 , ASP H:37 , SER H:39 , ASP H:77 , HOH H:92 , HOH H:96 , HOH H:98BINDING SITE FOR RESIDUE CA H 115
20CC2SOFTWAREASP H:36 , GLN H:53 , LYS H:78 , SER H:80 , HOH H:94 , HOH H:119 , HOH H:120 , HOH H:219BINDING SITE FOR RESIDUE CA H 116

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:9 -A:70
2B:9 -B:70
3C:9 -C:70
4D:9 -D:70
5E:9 -E:70
6F:9 -F:70
7G:9 -G:70
8H:9 -H:70

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HZB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HZB)

(-) Exons   (0, 0)

(no "Exon" information available for 3HZB)

(-) Sequences/Alignments

Asymmetric 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:86
 aligned with A5FC88_FLAJ1 | A5FC88 from UniProtKB/TrEMBL  Length:957

    Alignment length:86
                                   510       520       530       540       550       560       570       580      
         A5FC88_FLAJ1   501 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIA 586
               SCOP domains d3hzba_ A: automated matches                                                           SCOP domains
               CATH domains 3hzbA00 A:1-86 Crystallins                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee..eeehhhhhhhh........eeee....eeeeeeehhheeeeeee................eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 3hzb A   1 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIA  86
                                    10        20        30        40        50        60        70        80      


Chain B from PDB  Type:PROTEIN  Length:87
 aligned with A5FC88_FLAJ1 | A5FC88 from UniProtKB/TrEMBL  Length:957

    Alignment length:87
                                   510       520       530       540       550       560       570       580       
         A5FC88_FLAJ1   501 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIAN 587
               SCOP domains d3hzbb_ B: automated matches                                                            SCOP domains
               CATH domains 3hzbB00 B:1-87 Crystallins                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee..eeehhhhhhh.........eeee...eeeeeeeehhheeeeeee................eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3hzb B   1 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIAN  87
                                    10        20        30        40        50        60        70        80       


Chain C from PDB  Type:PROTEIN  Length:88
 aligned with A5FC88_FLAJ1 | A5FC88 from UniProtKB/TrEMBL  Length:957

    Alignment length:88
                                   510       520       530       540       550       560       570       580        
         A5FC88_FLAJ1   501 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIANG 588
               SCOP domains d3hzbc_ C: automated matches                                                             SCOP domains
               CATH domains 3hzbC00 C:1-88 Crystallins                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee..eeehhhhhhh.........eeee...eeeeeeee...eeeeeee................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3hzb C   1 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIANG  88
                                    10        20        30        40        50        60        70        80        


Chain D from PDB  Type:PROTEIN  Length:90
 aligned with A5FC88_FLAJ1 | A5FC88 from UniProtKB/TrEMBL  Length:957

    Alignment length:90
                                   510       520       530       540       550       560       570       580       590
         A5FC88_FLAJ1   501 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIANGTT 590
               SCOP domains d3hzbd_ D: automated matches                                                               SCOP domains
               CATH domains 3hzbD00 D:1-90 Crystallins                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee..eeehhhhhhh.........eeee...eeeeee.hhhhh..eeee................eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 3hzb D   1 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIANGTT  90
                                    10        20        30        40        50        60        70        80        90


Chain E from PDB  Type:PROTEIN  Length:90
 aligned with A5FC88_FLAJ1 | A5FC88 from UniProtKB/TrEMBL  Length:957

    Alignment length:90
                                   510       520       530       540       550       560       570       580       590
         A5FC88_FLAJ1   501 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIANGTT 590
               SCOP domains d3hzbe_ E: automated matches                                                               SCOP domains
               CATH domains 3hzbE00 E:1-90 Crystallins                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee..eeehhhhhhh.........eeee...eeeeee.hhhhh..eeee................eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 3hzb E   1 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIANGTT  90
                                    10        20        30        40        50        60        70        80        90


Chain F from PDB  Type:PROTEIN  Length:88
 aligned with A5FC88_FLAJ1 | A5FC88 from UniProtKB/TrEMBL  Length:957

    Alignment length:88
                                   510       520       530       540       550       560       570       580        
         A5FC88_FLAJ1   501 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIANG 588
               SCOP domains d3hzbf_ F: automated matches                                                             SCOP domains
               CATH domains 3hzbF00 F:1-88 Crystallins                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee..eeehhhhhhh.........eeee...eeeeeeee...eeeeeee................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3hzb F   1 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIANG  88
                                    10        20        30        40        50        60        70        80        


Chain G from PDB  Type:PROTEIN  Length:87
 aligned with A5FC88_FLAJ1 | A5FC88 from UniProtKB/TrEMBL  Length:957

    Alignment length:87
                                   510       520       530       540       550       560       570       580       
         A5FC88_FLAJ1   501 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIAN 587
               SCOP domains d3hzbg_ G: automated matches                                                            SCOP domains
               CATH domains 3hzbG00 G:1-87 Crystallins                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee..eeehhhhhhhh........eeee...eeeeeeeehhheeeeeee................eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3hzb G   1 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIAN  87
                                    10        20        30        40        50        60        70        80       


Chain H from PDB  Type:PROTEIN  Length:87
 aligned with A5FC88_FLAJ1 | A5FC88 from UniProtKB/TrEMBL  Length:957

    Alignment length:87
                                   510       520       530       540       550       560       570       580       
         A5FC88_FLAJ1   501 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIAN 587
               SCOP domains d3hzbh_ H: automated matches                                                            SCOP domains
               CATH domains 3hzbH00 H:1-87 Crystallins                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee..eeehhhhhhhh........eeee...eeeeeeeehhheeeeeee................eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3hzb H   1 DVITVYKDCNYTGFSGGLTIGDYNLARLNSLGVLNDDISSLRITQGYQAILYQDDNFGGASTVINSDNSCLNTTWNDKVSSIRVIAN  87
                                    10        20        30        40        50        60        70        80
   Legend:   → Mismatch (orange background)
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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, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HZB)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (A5FC88_FLAJ1 | A5FC88)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3hzb
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  A5FC88_FLAJ1 | A5FC88
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1nps 3hz2