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(-) Description

Title :  CRYSTAL STRUCTURE OF A XYLOSE ISOMERASE DOMAIN CONTAINING PROTEIN (STM4435) FROM SALMONELLA TYPHIMURIUM LT2 AT 2.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  18 May 07  (Deposition) - 05 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),C (1x)
Biol. Unit 6:  B (1x),D (1x)
Keywords :  Putative Cytoplasmic Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Cytoplasmic Protein (Np_463296. 1) From Salmonella Typhimurium Lt2 At 2. 40 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE CYTOPLASMIC PROTEIN
    Atcc: 700720
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_463296.1, STM4435
    Organism Scientific: SALMONELLA TYPHIMURIUM LT2
    Organism Taxid: 99287
    Strain: LT2, SGSC1412

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x) C (1x) 
Biological Unit 6 (1x):  B (1x) D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 38)

Asymmetric Unit (4, 38)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2MSE20Mod. Amino AcidSELENOMETHIONINE
3UNL4Ligand/IonUNKNOWN LIGAND
4ZN6Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3UNL1Ligand/IonUNKNOWN LIGAND
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3UNL1Ligand/IonUNKNOWN LIGAND
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3UNL1Ligand/IonUNKNOWN LIGAND
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3UNL1Ligand/IonUNKNOWN LIGAND
4ZN-1Ligand/IonZINC ION
Biological Unit 5 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3UNL1Ligand/IonUNKNOWN LIGAND
4ZN-1Ligand/IonZINC ION
Biological Unit 6 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3UNL1Ligand/IonUNKNOWN LIGAND
4ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:138 , ASP A:169 , HIS A:196 , GLU A:244 , UNL A:304BINDING SITE FOR RESIDUE ZN A 300
02AC2SOFTWAREGLU B:138 , ASP B:169 , HIS B:196 , GLU B:244 , UNL B:305BINDING SITE FOR RESIDUE ZN B 300
03AC3SOFTWAREGLU C:138 , ASP C:169 , HIS C:196 , GLU C:244 , UNL C:303BINDING SITE FOR RESIDUE ZN C 300
04AC4SOFTWAREGLU D:138 , ASP D:169 , HIS D:196 , GLU D:244 , UNL D:302BINDING SITE FOR RESIDUE ZN D 300
05AC5SOFTWAREASP A:126 , CL A:302 , CL A:303 , GLU C:81BINDING SITE FOR RESIDUE ZN A 301
06AC6SOFTWAREASP B:126 , CL B:303 , CL B:304 , GLU D:81BINDING SITE FOR RESIDUE ZN B 301
07AC7SOFTWAREARG D:148 , SER D:149BINDING SITE FOR RESIDUE CL D 301
08AC8SOFTWAREARG B:148BINDING SITE FOR RESIDUE CL B 302
09AC9SOFTWAREARG C:148 , SER C:149BINDING SITE FOR RESIDUE CL C 301
10BC1SOFTWAREARG C:130BINDING SITE FOR RESIDUE CL C 302
11BC2SOFTWAREZN A:301BINDING SITE FOR RESIDUE CL A 302
12BC3SOFTWARELYS A:122 , ZN A:301BINDING SITE FOR RESIDUE CL A 303
13BC4SOFTWAREZN B:301BINDING SITE FOR RESIDUE CL B 303
14BC5SOFTWAREGLU B:119 , LYS B:122 , ZN B:301BINDING SITE FOR RESIDUE CL B 304
15BC6SOFTWAREGLU A:138 , ASP A:169 , HIS A:172 , ASP A:211 , ARG A:214 , GLU A:244 , PHE A:246 , ZN A:300BINDING SITE FOR RESIDUE UNL A 304
16BC7SOFTWAREGLU B:138 , PHE B:142 , ASP B:169 , HIS B:172 , ASP B:211 , ARG B:214 , GLU B:244 , PHE B:246 , ZN B:300BINDING SITE FOR RESIDUE UNL B 305
17BC8SOFTWAREGLU C:138 , HIS C:172 , HIS C:196 , ASP C:211 , ARG C:214 , GLU C:244 , ZN C:300 , HOH C:375BINDING SITE FOR RESIDUE UNL C 303
18BC9SOFTWAREGLU D:138 , ASP D:169 , HIS D:172 , HIS D:196 , ASP D:211 , ARG D:214 , GLU D:244 , ZN D:300 , HOH D:370BINDING SITE FOR RESIDUE UNL D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q02)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asn A:70 -Ala A:71
2Tyr A:73 -Pro A:74
3Asn B:70 -Ala B:71
4Tyr B:73 -Pro B:74
5Asn C:70 -Ala C:71
6Tyr C:73 -Pro C:74
7Asn D:70 -Ala D:71
8Tyr D:73 -Pro D:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q02)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q02)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q02)

(-) 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:272
 aligned with Q8ZK48_SALTY | Q8ZK48 from UniProtKB/TrEMBL  Length:271

    Alignment length:272
                             1                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269  
         Q8ZK48_SALTY     - -MNIEKTRFCINRKIAPGLSIEAFFRLVKRLEFNKVELRNDMPSGSVTDDLNYNQVRNLAEKYGLEIVTINAVYPFNQLTEEVVKKTEGLLRDAQGVGARALVLCPLNDGTIVPPEVTVEAIKRLSDLFARYDIQGLVEPLGFRVSSLRSAVWAQQLIREAGSPFKVLLDTFHHHLYEEAEKEFASRIDISAIGLVHLSGVEDTRPTEALADEQRIMLSEKDVMQNYQQVQRLENMGYRGIYAFEPFSSQLASWSEAEIEEQINRSVSLLLQ 271
               SCOP domains -d2q02a1 A:1-271 Putative cytoplasmic protein STM4435                                                                                                                                                                                                                            SCOP domains
               CATH domains 2q02A00 A:0-271 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeee.hhh...hhhhhhhhhhhh...eeeee............hhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhh...eeeeehhhhhhh.....hhhhhhhhh.eeeeee.......hhhhhhhhhh.........hhhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q02 A   0 GmNIEKTRFCINRKIAPGLSIEAFFRLVKRLEFNKVELRNDmPSGSVTDDLNYNQVRNLAEKYGLEIVTINAVYPFNQLTEEVVKKTEGLLRDAQGVGARALVLCPLNDGTIVPPEVTVEAIKRLSDLFARYDIQGLVEPLGFRVSSLRSAVWAQQLIREAGSPFKVLLDTFHHHLYEEAEKEFASRIDISAIGLVHLSGVEDTRPTEALADEQRImLSEKDVmQNYQQVQRLENmGYRGIYAFEPFSSQLASWSEAEIEEQINRSVSLLLQ 271
                             |       9        19        29        39 |      49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      |219   |   229     | 239       249       259       269  
                             |                                      41-MSE                                                                                                                                                                        216-MSE  |         235-MSE                                
                             1-MSE                                                                                                                                                                                                                       223-MSE                                            


Chain B from PDB  Type:PROTEIN  Length:272
 aligned with Q8ZK48_SALTY | Q8ZK48 from UniProtKB/TrEMBL  Length:271

    Alignment length:272
                             1                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269  
         Q8ZK48_SALTY     - -MNIEKTRFCINRKIAPGLSIEAFFRLVKRLEFNKVELRNDMPSGSVTDDLNYNQVRNLAEKYGLEIVTINAVYPFNQLTEEVVKKTEGLLRDAQGVGARALVLCPLNDGTIVPPEVTVEAIKRLSDLFARYDIQGLVEPLGFRVSSLRSAVWAQQLIREAGSPFKVLLDTFHHHLYEEAEKEFASRIDISAIGLVHLSGVEDTRPTEALADEQRIMLSEKDVMQNYQQVQRLENMGYRGIYAFEPFSSQLASWSEAEIEEQINRSVSLLLQ 271
               SCOP domains d2q02b_ B: Putative cytoplasmic protein STM4435                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2q02B00 B:0-271 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeee.hhh...hhhhhhhhhhhh...eeeee............hhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhh....eeeeehhhhhhhhhhh.hhhhhhhhh.eeeeee.......hhhhhhhhhh.........hhhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q02 B   0 GmNIEKTRFCINRKIAPGLSIEAFFRLVKRLEFNKVELRNDmPSGSVTDDLNYNQVRNLAEKYGLEIVTINAVYPFNQLTEEVVKKTEGLLRDAQGVGARALVLCPLNDGTIVPPEVTVEAIKRLSDLFARYDIQGLVEPLGFRVSSLRSAVWAQQLIREAGSPFKVLLDTFHHHLYEEAEKEFASRIDISAIGLVHLSGVEDTRPTEALADEQRImLSEKDVmQNYQQVQRLENmGYRGIYAFEPFSSQLASWSEAEIEEQINRSVSLLLQ 271
                             |       9        19        29        39 |      49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      |219   |   229     | 239       249       259       269  
                             1-MSE                                  41-MSE                                                                                                                                                                        216-MSE  |         235-MSE                                
                                                                                                                                                                                                                                                         223-MSE                                            


Chain C from PDB  Type:PROTEIN  Length:271
 aligned with Q8ZK48_SALTY | Q8ZK48 from UniProtKB/TrEMBL  Length:271

    Alignment length:271
                                    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 
         Q8ZK48_SALTY     1 MNIEKTRFCINRKIAPGLSIEAFFRLVKRLEFNKVELRNDMPSGSVTDDLNYNQVRNLAEKYGLEIVTINAVYPFNQLTEEVVKKTEGLLRDAQGVGARALVLCPLNDGTIVPPEVTVEAIKRLSDLFARYDIQGLVEPLGFRVSSLRSAVWAQQLIREAGSPFKVLLDTFHHHLYEEAEKEFASRIDISAIGLVHLSGVEDTRPTEALADEQRIMLSEKDVMQNYQQVQRLENMGYRGIYAFEPFSSQLASWSEAEIEEQINRSVSLLLQ 271
               SCOP domains d2q02c_ C: Putative cytoplasmic protein STM4435                                                                                                                                                                                                                                 SCOP domains
               CATH domains -2q02C00 C:2-271 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeee.hhh...hhhhhhhhhhhh...eeeee............hhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhh.eeeeee.......hhhhhhhhhh.........hhhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q02 C   1 mNIEKTRFCINRKIAPGLSIEAFFRLVKRLEFNKVELRNDmPSGSVTDDLNYNQVRNLAEKYGLEIVTINAVYPFNQLTEEVVKKTEGLLRDAQGVGARALVLCPLNDGTIVPPEVTVEAIKRLSDLFARYDIQGLVEPLGFRVSSLRSAVWAQQLIREAGSPFKVLLDTFHHHLYEEAEKEFASRIDISAIGLVHLSGVEDTRPTEALADEQRImLSEKDVmQNYQQVQRLENmGYRGIYAFEPFSSQLASWSEAEIEEQINRSVSLLLQ 271
                            |       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 
                            1-MSE                                  41-MSE                                                                                                                                                                        216-MSE  |         235-MSE                                
                                                                                                                                                                                                                                                        223-MSE                                            


Chain D from PDB  Type:PROTEIN  Length:272
 aligned with Q8ZK48_SALTY | Q8ZK48 from UniProtKB/TrEMBL  Length:271

    Alignment length:272
                             1                                                                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269  
         Q8ZK48_SALTY     - -MNIEKTRFCINRKIAPGLSIEAFFRLVKRLEFNKVELRNDMPSGSVTDDLNYNQVRNLAEKYGLEIVTINAVYPFNQLTEEVVKKTEGLLRDAQGVGARALVLCPLNDGTIVPPEVTVEAIKRLSDLFARYDIQGLVEPLGFRVSSLRSAVWAQQLIREAGSPFKVLLDTFHHHLYEEAEKEFASRIDISAIGLVHLSGVEDTRPTEALADEQRIMLSEKDVMQNYQQVQRLENMGYRGIYAFEPFSSQLASWSEAEIEEQINRSVSLLLQ 271
               SCOP domains d2q02d_ D: Putative cytoplasmic protein STM4435                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2q02D00 D:0-271 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ------------------------AP_endonuc_2-2q02D01 D:24-222                                                                                                                                                                          ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------AP_endonuc_2-2q02D02 D:24-222                                                                                                                                                                          ------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------AP_endonuc_2-2q02D03 D:24-222                                                                                                                                                                          ------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------AP_endonuc_2-2q02D04 D:24-222                                                                                                                                                                          ------------------------------------------------- Pfam domains (4)
         Sec.struct. author ....hhh.eeee.hhh...hhhhhhhhhhhh...eeeee............hhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhh.eeeeee.......hhhhhhhhhh.........hhhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q02 D   0 GmNIEKTRFCINRKIAPGLSIEAFFRLVKRLEFNKVELRNDmPSGSVTDDLNYNQVRNLAEKYGLEIVTINAVYPFNQLTEEVVKKTEGLLRDAQGVGARALVLCPLNDGTIVPPEVTVEAIKRLSDLFARYDIQGLVEPLGFRVSSLRSAVWAQQLIREAGSPFKVLLDTFHHHLYEEAEKEFASRIDISAIGLVHLSGVEDTRPTEALADEQRImLSEKDVmQNYQQVQRLENmGYRGIYAFEPFSSQLASWSEAEIEEQINRSVSLLLQ 271
                             |       9        19        29        39 |      49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      |219   |   229     | 239       249       259       269  
                             1-MSE                                  41-MSE                                                                                                                                                                        216-MSE  |         235-MSE                                
                                                                                                                                                                                                                                                         223-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8ZK48_SALTY | Q8ZK48)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  2q02
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  Q8ZK48_SALTY | Q8ZK48
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 Related Entries

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

UniProtKB/TrEMBL
        Q8ZK48_SALTY | Q8ZK48: 4hgx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Q02)