4FEY | pdb_00004fey

An X-ray Structure of a Putative Phosphogylcerate Kinase with Bound ADP from Francisella tularensis subsp. tularensis SCHU S4

PDB DOI: https://doi.org/10.2210/pdb4FEY/pdb

Classification: TRANSFERASE
Organism(s): Francisella tularensis subsp. tularensis SCHU S4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-05-30 Released: 2012-06-13
Deposition Author(s): Brunzelle, J.S., Wawrzak, Z., Skarina, T., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.248 (Depositor), 0.276 (DCC)
R-Value Work:
0.193 (Depositor)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4FEY

Ligand Structure Quality Assessment

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

Literature

An X-ray Structure of a Putative Phosphogylcerate Kinase with Bound ADP from Francisella tularensis subsp. tularensis SCHU S4

Brunzelle, J.S., Wawrzak, Z., Skarina, T., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases

To be published.

Macromolecule Content

Total Structure Weight: 42.68 kDa
Atom Count: 3,101
Modeled Residue Count: 392
Deposited Residue Count: 395
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	A	395	Francisella tularensis subsp. tularensis SCHU S4	Mutation(s): 0 Gene Names: FTT_1367c, pgk EC: 2.7.2.3
UniProt
Find proteins for Q5NF76 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NF76 Go to UniProtKB: Q5NF76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NF76
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.248 (Depositor), 0.276 (DCC)
R-Value Work: 0.193 (Depositor)
R-Value Observed: 0.196 (Depositor)

Diffraction Data:

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.616	α = 90
b = 66.616	β = 90
c = 206.524	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
PHASER	phasing
PHENIX	model building
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Brunzelle, J.S.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, 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.