7E2A | pdb_00007e2a

GDPD mutant from Pyrococcus furiosus DSM 3638

PDB DOI: https://doi.org/10.2210/pdb7E2A/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus furiosus DSM 3638
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-02-05 Released: 2022-02-09
Deposition Author(s): Wang, Y.H., Wang, J., Wang, F.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.231 (Depositor), 0.231 (DCC)
R-Value Work:
0.185 (Depositor), 0.187 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7E2A

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of glycerophoshphodiester phospodiesterase D60A mutant from Pyrococcus furiosus DSM

Wang, Y.H., Wang, J., Wang, F.H.

To be published.

Macromolecule Content

Total Structure Weight: 29.37 kDa
Atom Count: 2,108
Modeled Residue Count: 253
Deposited Residue Count: 255
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphodiester phosphodiesterase	A	255	Pyrococcus furiosus DSM 3638	Mutation(s): 1 Gene Names: PF2003
UniProt
Find proteins for Q8TZI9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZI9 Go to UniProtKB: Q8TZI9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TZI9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.231 (Depositor), 0.231 (DCC)
R-Value Work: 0.185 (Depositor), 0.187 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.89	α = 90
b = 69.6	β = 90
c = 89.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31725022
National Natural Science Foundation of China (NSFC)	China	31972014

Revision History (Full details and data files)

Version 1.0: 2022-02-09
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.