3KS5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF PUTATIVE GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE (17743486) FROM AGROBACTERIUM TUMEFACIENS STR. C58 (DUPONT) AT 2.05 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 :   2.05

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (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 2. 05 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE
	Chains	:	A, B
	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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 37)

No.	Name	Count	Type	Full Name
1	ACT	7	Ligand/Ion	ACETATE ION
2	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	FE	2	Ligand/Ion	FE (III) ION
4	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
3	FE	-1	Ligand/Ion	FE (III) ION
4	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 17)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
3	FE	-1	Ligand/Ion	FE (III) ION
4	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:34 , ASP A:36 , GLU A:104 , ACT A:251 , ACT A:252 , HOH A:268	BINDING SITE FOR RESIDUE FE A 250
02	AC2	SOFTWARE	HIS A:7 , ARG A:8 , HIS A:49 , GLU A:104 , LYS A:106 , FE A:250 , ACT A:252 , HOH A:288	BINDING SITE FOR RESIDUE ACT A 251
03	AC3	SOFTWARE	HIS A:7 , GLU A:34 , GLU A:104 , LEU A:158 , THR A:229 , FE A:250 , ACT A:251 , HOH A:316	BINDING SITE FOR RESIDUE ACT A 252
04	AC4	SOFTWARE	GLN A:165	BINDING SITE FOR RESIDUE ACT A 253
05	AC5	SOFTWARE	MSE A:196 , GLN A:200 , ASP A:205 , PHE A:206 , LYS A:226	BINDING SITE FOR RESIDUE ACT A 254
06	AC6	SOFTWARE	SER A:160 , PRO A:161 , SER A:162 , SER B:162 , GLN B:166	BINDING SITE FOR RESIDUE EDO A 255
07	AC7	SOFTWARE	ARG A:8 , ASP A:16 , HIS A:48 , HIS A:49 , ASP A:50 , THR A:56 , HOH A:286 , HOH A:301	BINDING SITE FOR RESIDUE EDO A 256
08	AC8	SOFTWARE	GLU A:174 , MSE B:1 , GLU B:31 , ARG B:240 , ARG B:244 , HOH B:276 , HOH B:374	BINDING SITE FOR RESIDUE EDO A 257
09	AC9	SOFTWARE	LEU A:167 , GLY A:168 , GLY A:170 , ALA A:171 , HOH A:315 , ALA B:142 , HOH B:414	BINDING SITE FOR RESIDUE EDO A 258
10	BC1	SOFTWARE	GLY A:0 , MSE A:1 , THR A:2 , GLY A:224 , HOH A:357	BINDING SITE FOR RESIDUE EDO A 259
11	BC2	SOFTWARE	GLU B:34 , ASP B:36 , GLU B:104 , ACT B:251 , ACT B:252 , HOH B:260	BINDING SITE FOR RESIDUE FE B 250
12	BC3	SOFTWARE	HIS B:7 , ARG B:8 , HIS B:49 , GLU B:104 , LYS B:106 , FE B:250 , ACT B:252 , HOH B:382	BINDING SITE FOR RESIDUE ACT B 251
13	BC4	SOFTWARE	HIS B:7 , GLU B:34 , GLU B:104 , LEU B:158 , TRP B:209 , THR B:229 , FE B:250 , ACT B:251 , HOH B:297	BINDING SITE FOR RESIDUE ACT B 252
14	BC5	SOFTWARE	LYS A:106 , PRO A:107 , PHE A:139 , HOH A:356 , GLN B:165 , GLN B:166	BINDING SITE FOR RESIDUE ACT B 253
15	BC6	SOFTWARE	ASP A:145 , HOH A:322 , LEU B:167 , GLY B:168 , GLY B:170 , ALA B:171 , HOH B:428	BINDING SITE FOR RESIDUE EDO B 254
16	BC7	SOFTWARE	ARG B:8 , ASP B:16 , HIS B:49 , ASP B:50 , THR B:56 , HOH B:271	BINDING SITE FOR RESIDUE EDO B 255
17	BC8	SOFTWARE	GLU A:174 , ALA B:178 , THR B:241 , ARG B:244	BINDING SITE FOR RESIDUE EDO B 256
18	BC9	SOFTWARE	PRO B:113 , ALA B:142 , GLU B:146 , HOH B:401	BINDING SITE FOR RESIDUE EDO B 257
19	CC1	SOFTWARE	PRO B:161 , ASP B:189	BINDING SITE FOR RESIDUE EDO B 258

(no "SS Bond" information available for 3KS5)

(no "Cis Peptide Bond" information available for 3KS5)

(no "SAP(SNP)/Variant" information available for 3KS5)

(no "PROSITE Motif" information available for 3KS5)

(no "Exon" information available for 3KS5)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:247
 aligned with A9CLR1_AGRFC | A9CLR1 from UniProtKB/TrEMBL  Length:249

    Alignment length:247
                             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     - -MTRIASHRGGTLEFGDSTPHGFTATAAMALEEVEFDLHPTADGAIVVHHDPTLDATTDMTGAIVDMTLAKVKTATIRYGAGSHPMTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSMLERTTFSSFLLASMDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLMAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRME 246
               SCOP domains d3ks5a_ A: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh..hhhhhhhhhh....eeeeeeee.....eee..............hhhhhhhhhhhhh...........hhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks5 A   0 GmTRIASHRGGTLEFGDSTPHGFTATAAmALEEVEFDLHPTADGAIVVHHDPTLDATTDmTGAIVDmTLAKVKTATIRYGAGSHPmTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSmLERTTFSSFLLASmDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLmAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRmE 246
                             |       9        19        29        39        49        59      | 69        79     |  89        99       109       119       129|      139    |  149       159       169       179       189      |199       209       219       229       239     | 
                             |                         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:248
 aligned with A9CLR1_AGRFC | A9CLR1 from UniProtKB/TrEMBL  Length:249

    Alignment length:248
                             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     - -MTRIASHRGGTLEFGDSTPHGFTATAAMALEEVEFDLHPTADGAIVVHHDPTLDATTDMTGAIVDMTLAKVKTATIRYGAGSHPMTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSMLERTTFSSFLLASMDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLMAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRMEA 247
               SCOP domains d3ks5b_ B: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh..hhhhhhhhhh....eeeeeeee.....eee..............hhhhhhhhhhh............eehhhhhhhhh....eeeeee..........hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ks5 B   0 GmTRIASHRGGTLEFGDSTPHGFTATAAmALEEVEFDLHPTADGAIVVHHDPTLDATTDmTGAIVDmTLAKVKTATIRYGAGSHPmTLEELCALYVDSHVNFRCEIKPGVDGLPYEGFVALVIAGLERHSmLERTTFSSFLLASmDELWKATTRPRLWLVSPSVLQQLGPGAVIETAIAHSIHEIGVHIDTADAGLmAQVQAAGLDFGCWAAHTPSQITKALDLGVKVFTTDRPTLAIALRTEHRmEA 247
                             |       9        19        29        39        49        59      | 69        79     |  89        99       109       119       129|      139    |  149       159       169       179       189      |199       209       219       229       239     |  
                             |                         28-MSE                         59-MSE 66-MSE             85-MSE                                      130-MSE       144-MSE                                             196-MSE                                          245-MSE
                             1-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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: PLC-like phosphodiesterases (46)

Family: automated matches (11)

Protein domain: automated matches (11)

Agrobacterium tumefaciens [TaxId: 176299] (2)

1a	d3ks5a_	A:
1b	d3ks5b_	B:

(no "CATH Domain" information available for 3KS5)

(no "Pfam Domain" information available for 3KS5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ks5)

Biological Units
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 37)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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