3KS5

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution

PDB DOI: https://doi.org/10.2210/pdb3KS5/pdb

Classification: HYDROLASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-20 Released: 2009-12-08
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.244
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 55.7 kDa
Atom Count: 4,249
Modelled Residue Count: 495
Deposited Residue Count: 500
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphoryl diester phosphodiesterase	A, B	250	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: 17743486, AGR_pAT_81, Atu5061, glpQ
UniProt
Find proteins for A9CLR1 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CLR1 Go to UniProtKB: A9CLR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9CLR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] N [auth B] D [auth A], E [auth A], F [auth A], G [auth A], N [auth B], O [auth B], P [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B]	C [auth A], M [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.244
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: P 4₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M33KS5

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.153	α = 90
b = 84.153	β = 90
c = 214.882	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHARP	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-12-08

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-12-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations

Prepare Data

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Deposit Data

Help and Resources

3KS5

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 2.05 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)