3N0V

Crystal structure of a formyltetrahydrofolate deformylase (PP_0327) from PSEUDOMONAS PUTIDA KT2440 at 2.25 A resolution

PDB DOI: https://doi.org/10.2210/pdb3N0V/pdb

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

Deposited: 2010-05-14 Released: 2010-06-16
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.274
R-Value Work: 0.222
R-Value Observed: 0.225

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a formyltetrahydrofolate deformylase (PP_0327) from PSEUDOMONAS PUTIDA KT2440 at 2.25 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 131.5 kDa
Atom Count: 9,481
Modelled Residue Count: 1,117
Deposited Residue Count: 1,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formyltetrahydrofolate deformylase	A, B, C, D	286	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: purU-1, PP0327, PP_0327
UniProt
Find proteins for Q88R07 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88R07 Go to UniProtKB: Q88R07
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q88R07
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.274
R-Value Work: 0.222
R-Value Observed: 0.225
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M33N0V

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.213	α = 90
b = 93.965	β = 101.38
c = 97.129	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-06-16

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.