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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A HYDROLASE FROM PSEUDOMONAS SYRINGAE
 
Authors :  Z. Zhang, B. Syed Ibrahim, S. K. Burley, S. Swaminathan, New York Sgx Center For Structural Genomics (Nysgxrc)
Date :  25 May 11  (Deposition) - 13 Jul 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,E,F  (1x)
Biol. Unit 3:  C,D,F  (1x)
Keywords :  Structural Genomics, Psi-2, Hydrolase, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, B. Syed Ibrahim, S. K. Burley, S. Swaminathan
The Crystal Structure Of A Hydrolase From Pseudomonas Syringae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYDROLASE, HALOACID DEHALOGENASE-LIKE FAMILY
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)-CODEN+RIL(P)-STRATAGENE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 105-326
    Gene: PSPTO0276, PSPTO_0276
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. TOMATO
    Organism Taxid: 323

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C E 
Biological Unit 2 (1x):  B  EF
Biological Unit 3 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 36)

Asymmetric Unit (2, 36)
No.NameCountTypeFull Name
1CA9Ligand/IonCALCIUM ION
2MSE27Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 14)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:113 , ASP A:115 , ASP A:273 , HOH A:355 , HOH A:356 , HOH A:360BINDING SITE FOR RESIDUE CA A 4
2AC2SOFTWAREHOH B:12 , ASP B:113 , ASP B:115 , ASP B:273 , HOH B:343 , HOH B:344BINDING SITE FOR RESIDUE CA B 2
3AC3SOFTWAREGLY B:295 , ASP B:297 , HOH B:358 , HOH B:359 , HOH B:360 , GLY F:295BINDING SITE FOR RESIDUE CA B 7
4AC4SOFTWAREASP C:113 , ASP C:115 , ASP C:273 , HOH C:356 , HOH C:357 , HOH C:358BINDING SITE FOR RESIDUE CA C 5
5AC5SOFTWAREGLY C:295 , ASP C:297 , HOH C:359 , HOH C:361 , HOH C:362 , GLY D:295BINDING SITE FOR RESIDUE CA C 9
6AC6SOFTWAREHOH D:17 , ASP D:113 , ASP D:115 , ASP D:273 , HOH D:353 , HOH D:354BINDING SITE FOR RESIDUE CA D 6
7AC7SOFTWAREHOH E:45 , ASP E:113 , ASP E:115 , ASP E:273 , HOH E:346 , HOH E:349BINDING SITE FOR RESIDUE CA E 1
8AC8SOFTWAREGLY A:295 , HOH A:362 , HOH A:363 , GLY E:295 , HOH E:363 , HOH E:364BINDING SITE FOR RESIDUE CA E 8
9AC9SOFTWAREASP F:113 , ASP F:115 , ASP F:273 , HOH F:355 , HOH F:356 , HOH F:357BINDING SITE FOR RESIDUE CA F 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S6J)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Lys A:248 -Pro A:249
2Lys B:248 -Pro B:249
3Thr C:164 -Gly C:165
4Lys C:248 -Pro C:249
5Lys D:248 -Pro D:249
6Lys E:248 -Pro E:249
7Lys F:248 -Pro F:249

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S6J)

(-) Exons   (0, 0)

(no "Exon" information available for 3S6J)

(-) 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:216
 aligned with Q88AV7_PSESM | Q88AV7 from UniProtKB/TrEMBL  Length:327

    Alignment length:220
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325
         Q88AV7_PSESM   106 PQTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAMWRIHRKIGMSGGLMLKSLSRETGMSITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDMLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
               SCOP domains d3s6ja_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eehhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhh----.hhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhh...eeee...hhhhhhhhhhh.........eehhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.hhh.hhhhhhhh...eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s6j A 106 PQTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAmWRIHRKIGmSGGLmLKSLSRE----ITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDmLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
                                   115       125       135      |145     | 155|      | -  |    175       185       195       205       215       225       235       245       255       265       275  |    285       295       305       315       325
                                                              142-MSE  151-MSE|    163  168                                                                                                           278-MSE                                           
                                                                            156-MSE                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with Q88AV7_PSESM | Q88AV7 from UniProtKB/TrEMBL  Length:327

    Alignment length:219
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         
         Q88AV7_PSESM   107 QTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAMWRIHRKIGMSGGLMLKSLSRETGMSITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDMLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
               SCOP domains d3s6jb_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eehhhhhhhhhhhhhhh.....hhhhhhh..........----------...hhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhh...eeee...hhhhhhhhhhhh........eehhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.hhh.hhhhhhhh...eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s6j B 107 QTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAmWRIHRKIGmSGGLmL----------ITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDmLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
                                   116       126       136     | 146    |  156|        - |     176       186       196       206       216       226       236       246       256       266       276 |     286       296       306       316         
                                                             142-MSE  151-MSE||        168                                                                                                           278-MSE                                           
                                                                           156-MSE                                                                                                                                                                     
                                                                            157                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:212
 aligned with Q88AV7_PSESM | Q88AV7 from UniProtKB/TrEMBL  Length:327

    Alignment length:219
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         
         Q88AV7_PSESM   107 QTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAMWRIHRKIGMSGGLMLKSLSRETGMSITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDMLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
               SCOP domains d3s6jc_ C: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eehhhhhhhhhhhhhhhh....hhhhhhh.........-------.....hhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhh...eeee...hhhhhhhhhhhh..hhhhh.eehhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.hhh.hhhhhhhh...eee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s6j C 107 QTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAmWRIHRKIGmSGGLm-------TGmSITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDmLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
                                   116       126       136     | 146    |  156       166       176       186       196       206       216       226       236       246       256       266       276 |     286       296       306       316         
                                                             142-MSE  151-MSE|     164 |                                                                                                             278-MSE                                           
                                                                           156-MSE   166-MSE                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:216
 aligned with Q88AV7_PSESM | Q88AV7 from UniProtKB/TrEMBL  Length:327

    Alignment length:219
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         
         Q88AV7_PSESM   107 QTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAMWRIHRKIGMSGGLMLKSLSRETGMSITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDMLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
               SCOP domains d3s6jd_ D: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eehhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhh---.hhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhh...eeee...hhhhhhhhhhh.........eehhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.hhh.hhhhhhhh.eeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s6j D 107 QTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAmWRIHRKIGmSGGLmLKSLSRET---ITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDmLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
                                   116       126       136     | 146    |  156       | - |     176       186       196       206       216       226       236       246       256       266       276 |     286       296       306       316         
                                                             142-MSE  151-MSE|     164 168                                                                                                           278-MSE                                           
                                                                           156-MSE                                                                                                                                                                     


Chain E from PDB  Type:PROTEIN  Length:220
 aligned with Q88AV7_PSESM | Q88AV7 from UniProtKB/TrEMBL  Length:327

    Alignment length:220
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325
         Q88AV7_PSESM   106 PQTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAMWRIHRKIGMSGGLMLKSLSRETGMSITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDMLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
               SCOP domains d3s6je_ E: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eehhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhh...eeee...hhhhhhhhhhhh..hhhhh.eehhhhh......hhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh..eeeee.hhh.hhhhhhhh...eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s6j E 106 PQTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAmWRIHRKIGmSGGLmLKSLSRETGmSITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDmLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
                                   115       125       135      |145     | 155|      165|      175       185       195       205       215       225       235       245       255       265       275  |    285       295       305       315       325
                                                              142-MSE  151-MSE|       166-MSE                                                                                                         278-MSE                                           
                                                                            156-MSE                                                                                                                                                                     


Chain F from PDB  Type:PROTEIN  Length:219
 aligned with Q88AV7_PSESM | Q88AV7 from UniProtKB/TrEMBL  Length:327

    Alignment length:219
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316         
         Q88AV7_PSESM   107 QTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAMWRIHRKIGMSGGLMLKSLSRETGMSITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDMLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
               SCOP domains d3s6jf_ F: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eehhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhh...eeee...hhhhhhhhhhhh..hhhhh.eehhhhh......hhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.hhh.hhhhhhhh...eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s6j F 107 QTSFIFDLDGTLTDSVYQNVAAWKEALDAENIPLAmWRIHRKIGmSGGLmLKSLSRETGmSITDEQAERLSEKHAQAYERLQHQIIALPGAVELLETLDKENLKWCIATSGGIDTATINLKALKLDINKINIVTRDDVSYGKPDPDLFLAAAKKIGAPIDECLVIGDAIWDmLAARRCKATGVGLLSGGYDIGELERAGALRVYEDPLDLLNHLDEIAS 325
                                   116       126       136     | 146    |  156       166       176       186       196       206       216       226       236       246       256       266       276 |     286       296       306       316         
                                                             142-MSE  151-MSE|       166-MSE                                                                                                         278-MSE                                           
                                                                           156-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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S6J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S6J)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q88AV7_PSESM | Q88AV7)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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