3KS6 | pdb_00003ks6

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.80 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.205 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3KS6

This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 109.81 kDa 
  • Atom Count: 9,129 
  • Modeled Residue Count: 993 
  • Deposited Residue Count: 1,000 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycerophosphoryl diester phosphodiesterase
A, B, C, D
250Agrobacterium fabrum str. C58Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CLR1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG


Download:Ideal Coordinates CCD File
J [auth A],
U [auth D]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
M [auth B]
N [auth B]
Q [auth C]
H [auth A],
I [auth A],
M [auth B],
N [auth B],
Q [auth C],
T [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL


Download:Ideal Coordinates CCD File
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG


Download:Ideal Coordinates CCD File
F [auth A],
L [auth B],
P [auth C],
S [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL

Query on UNL


Download:Ideal Coordinates CCD File
E [auth A],
K [auth B],
O [auth C],
R [auth D]		Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.205 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.427α = 90
b = 99.797β = 90
c = 134.656γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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
  • Version 1.5: 2024-11-06
    Changes: Data collection, Refinement description, Structure summary