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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (17743486) FROM AGROBACTERIUM TUMEFACIENS STR. C58 (DUPONT) AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 Nov 09  (Deposition) - 08 Dec 09  (Release) - 08 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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)
Keywords :  Putative Glycerophosphoryl Diester Phosphodiesterase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Plasmid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Glycerophosphoryl Diester Phosphodiesterase (17743486) From Agrobacterium Tumefaciens Str. C58 (Dupont) At 1. 80 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
    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: 17743486, AGR_PAT_81, ATU5061, GLPQ
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR. C58
    Organism Taxid: 176299
    Strain: C58 / ATCC 33970

 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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 53)

Asymmetric Unit (6, 53)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3MG4Ligand/IonMAGNESIUM ION
4MSE36Mod. Amino AcidSELENOMETHIONINE
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
6UNL4Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (4, 13)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MSE9Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
6UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MSE9Mod. Amino AcidSELENOMETHIONINE
5PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
6UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 3 (3, 11)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MSE9Mod. Amino AcidSELENOMETHIONINE
5PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
6UNL1Ligand/IonUNKNOWN LIGAND
Biological Unit 4 (4, 12)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4MSE9Mod. Amino AcidSELENOMETHIONINE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
6UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:34 , ASP A:36 , GLU A:104 , HOH A:256 , HOH A:290BINDING SITE FOR RESIDUE MG A 251
02AC2SOFTWAREMSE A:1 , THR A:2 , ARG A:244 , HOH B:342BINDING SITE FOR RESIDUE CL A 252
03AC3SOFTWAREHIS A:7 , ARG A:8 , ACT A:254 , HOH A:290 , HOH A:651BINDING SITE FOR RESIDUE ACT A 253
04AC4SOFTWARELYS A:106 , PHE A:139 , ACT A:253 , HOH A:288 , HOH A:359BINDING SITE FOR RESIDUE ACT A 254
05AC5SOFTWAREALA A:178 , HIS A:179 , GLU D:174BINDING SITE FOR RESIDUE PEG A 255
06AC6SOFTWAREGLU B:34 , ASP B:36 , GLU B:104 , HOH B:263 , HOH B:265BINDING SITE FOR RESIDUE MG B 251
07AC7SOFTWAREHIS B:7 , ARG B:8 , PHE B:139 , HOH B:265 , HOH B:525BINDING SITE FOR RESIDUE ACT B 252
08AC8SOFTWAREASP B:145 , ALA B:178 , HIS B:179 , ARG B:244 , MSE B:245 , HOH B:1079 , GLU C:174BINDING SITE FOR RESIDUE ACT B 253
09AC9SOFTWAREGLU C:34 , ASP C:36 , GLU C:104 , HOH C:261 , HOH C:276BINDING SITE FOR RESIDUE MG C 251
10BC1SOFTWAREHIS C:7 , ARG C:8 , HOH C:276 , HOH C:476BINDING SITE FOR RESIDUE ACT C 252
11BC2SOFTWAREGLU D:34 , ASP D:36 , GLU D:104 , HOH D:278 , HOH D:282BINDING SITE FOR RESIDUE MG D 251
12BC3SOFTWAREHIS D:7 , ARG D:8 , HOH D:282 , HOH D:786BINDING SITE FOR RESIDUE ACT D 252
13BC4SOFTWAREGLU A:174 , TRP D:148 , ALA D:178 , HIS D:179 , SER D:180BINDING SITE FOR RESIDUE PEG D 253

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KS6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KS6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KS6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KS6)

(-) Exons   (0, 0)

(no "Exon" information available for 3KS6)

(-) 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:250
 aligned with A9CLR1_AGRFC | A9CLR1 from UniProtKB/TrEMBL  Length:249

    Alignment length:250
                             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
         A9CLR1_AGRFC     - -MTRIASHRGGTLEFGDSTPHGFTATAAMALEEVEFDLHPTADGAIVVHHDPTLDATTDMTGAIVDMTLAKVKTATIRYGAGSHPMTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSMLERTTFSSFLLASMDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLMAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRMEASV 249
               SCOP domains d3ks6a_ A: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh..hhhhhhhhhh....eeeeeeee.....eee..............hhhhhhhhhhhhh..........eehhhhhhhhh....eeeeee..........hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks6 A   0 GmTRIASHRGGTLEFGDSTPHGFTATAAmALEEVEFDLHPTADGAIVVHHDPTLDATTDmTGAIVDmTLAKVKTATIRYGAGSHPmTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSmLERTTFSSFLLASmDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLmAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRmEASV 249
                             |       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
                             |                         28-MSE                         59-MSE 66-MSE             85-MSE                                      130-MSE       144-MSE                                             196-MSE                                          245-MSE
                             1-MSE                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with A9CLR1_AGRFC | A9CLR1 from UniProtKB/TrEMBL  Length:249

    Alignment length:249
                             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         
         A9CLR1_AGRFC     - -MTRIASHRGGTLEFGDSTPHGFTATAAMALEEVEFDLHPTADGAIVVHHDPTLDATTDMTGAIVDMTLAKVKTATIRYGAGSHPMTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSMLERTTFSSFLLASMDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLMAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRMEAS 248
               SCOP domains d3ks6b_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh..hhhhhhhhhh....eeeeeeee.....eee..............hhhhhhhhhhhhh..........eehhhhhhh......eeeeee..........hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks6 B   0 GmTRIASHRGGTLEFGDSTPHGFTATAAmALEEVEFDLHPTADGAIVVHHDPTLDATTDmTGAIVDmTLAKVKTATIRYGAGSHPmTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSmLERTTFSSFLLASmDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLmAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRmEAS 248
                             |       9        19        29        39        49        59      | 69        79     |  89        99       109       119       129|      139    |  149       159       169       179       189      |199       209       219       229       239     |   
                             1-MSE                     28-MSE                         59-MSE 66-MSE             85-MSE                                      130-MSE       144-MSE                                             196-MSE                                          245-MSE


Chain C from PDB  Type:PROTEIN  Length:248
 aligned with A9CLR1_AGRFC | A9CLR1 from UniProtKB/TrEMBL  Length:249

    Alignment length:248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
         A9CLR1_AGRFC     1 MTRIASHRGGTLEFGDSTPHGFTATAAMALEEVEFDLHPTADGAIVVHHDPTLDATTDMTGAIVDMTLAKVKTATIRYGAGSHPMTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSMLERTTFSSFLLASMDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLMAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRMEAS 248
               SCOP domains d3ks6c_ C: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhh..hhhhhhhhhh....eeeeeeee.....eee..............hhhhhhhhhhhhh...........hhhhhhhhhh....eeeeee..........hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks6 C   1 mTRIASHRGGTLEFGDSTPHGFTATAAmALEEVEFDLHPTADGAIVVHHDPTLDATTDmTGAIVDmTLAKVKTATIRYGAGSHPmTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSmLERTTFSSFLLASmDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLmAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRmEAS 248
                            |       10        20       |30        40        50        60     |  70        80    |   90       100       110       120       130       140   |   150       160       170       180       190     | 200       210       220       230       240    |   
                            |                         28-MSE                         59-MSE 66-MSE             85-MSE                                      130-MSE       144-MSE                                             196-MSE                                          245-MSE
                            1-MSE                                                                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:246
 aligned with A9CLR1_AGRFC | A9CLR1 from UniProtKB/TrEMBL  Length:249

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
         A9CLR1_AGRFC     1 MTRIASHRGGTLEFGDSTPHGFTATAAMALEEVEFDLHPTADGAIVVHHDPTLDATTDMTGAIVDMTLAKVKTATIRYGAGSHPMTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSMLERTTFSSFLLASMDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLMAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRME 246
               SCOP domains d3ks6d_ D: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..hhhhhh..hhhhhhhhhh....eeeeeeee.....eee..............hhhhhhhhhhhh............hhhhhhhhhh....eeeeee..........hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ks6 D   1 mTRIASHRGGTLEFGDSTPHGFTATAAmALEEVEFDLHPTADGAIVVHHDPTLDATTDmTGAIVDmTLAKVKTATIRYGAGSHPmTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSmLERTTFSSFLLASmDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLmAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRmE 246
                            |       10        20       |30        40        50        60     |  70        80    |   90       100       110       120       130       140   |   150       160       170       180       190     | 200       210       220       230       240    | 
                            |                         28-MSE                         59-MSE 66-MSE             85-MSE                                      130-MSE       144-MSE                                             196-MSE                                          245-MSE
                            1-MSE
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KS6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KS6)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A9CLR1_AGRFC | A9CLR1)
molecular function
    GO:0008889    glycerophosphodiester phosphodiesterase activity    Catalysis of the reaction: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

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 Related Entries

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        A9CLR1_AGRFC | A9CLR1: 3ks5

(-) Related Entries Specified in the PDB File

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