1ZCC

Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens str.C58

• PDB DOI: https://doi.org/10.2210/pdb1ZCC/pdb

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


• Deposited: 2005-04-11 Released: 2005-05-03 
• Deposition Author(s): Krishnamurthy, N.R., Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.244 
• R-Value Observed: 0.244 

Literature

Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit.

Rao, K.N., Bonanno, J.B., Burley, S.K., Swaminathan, S.

(2006) Proteins 65: 514-518

• PubMed: 16909422 
• DOI: https://doi.org/10.1002/prot.21079
• Primary Citation of Related Structures:  
  1ZCC

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Organizational Affiliation: 

Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 165.09 kDa 
• Atom Count: 10,986 
• Modelled Residue Count: 1,400 
• Deposited Residue Count: 1,488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerophosphodiester phosphodiesterase	A, B, C, D, E, F	248	Agrobacterium fabrum str. C58	Mutation(s): 0
UniProt
Find proteins for A9CG82 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CG82  Go to UniProtKB:  A9CG82

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.281 
• R-Value Work: 0.244 
• R-Value Observed: 0.244 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.56	α = 90
b = 140.22	β = 90.53
c = 88.6	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-03 
Deposition Author(s): Krishnamurthy, N.R., Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-05-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references