4H17 | pdb_00004h17

Crystal structure of an isochorismatase (PP1826) from Pseudomonas putida KT2440 at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4H17/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-10 Released: 2012-11-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

Crystal structure of an isochorismatase (PP1826) from Pseudomonas putida KT2440 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Macromolecule Content 

• Total Structure Weight: 44.16 kDa 
• Atom Count: 3,638 
• Modeled Residue Count: 391 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase, isochorismatase family	A, B	197	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: PP_1826
UniProt
Find proteins for Q88LV1 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88LV1  Go to UniProtKB:  Q88LV1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], H [auth A], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34H17

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.169	α = 90
b = 49.348	β = 90
c = 156.593	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary