3S6J | pdb_00003s6j

The crystal structure of a hydrolase from Pseudomonas syringae

• PDB DOI: https://doi.org/10.2210/pdb3S6J/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas syringae pv. tomato
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-25 Released: 2011-07-13 
• Deposition Author(s): Zhang, Z., Syed Ibrahim, B., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.243 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

The crystal structure of a hydrolase from Pseudomonas syringae

Zhang, Z., Syed Ibrahim, B., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 156.8 kDa 
• Atom Count: 10,211 
• Modeled Residue Count: 1,292 
• Deposited Residue Count: 1,398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase, haloacid dehalogenase-like family	A, B, C, D, E, F	233	Pseudomonas syringae pv. tomato	Mutation(s): 0  Gene Names: PSPTO0276, PSPTO_0276
UniProt
Find proteins for Q88AV7 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q88AV7  Go to UniProtKB:  Q88AV7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth E], N [auth E], O [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.243 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.535	α = 59.77
b = 74.887	β = 67.49
c = 75.113	γ = 88

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Zhang, Z., Syed Ibrahim, B., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2011-07-20
  Changes: Structure summary
• Version 1.2: 2020-01-29
  Changes: Database references, Derived calculations
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Structure summary