3KWM | pdb_00003kwm

Crystal structure of ribose-5-isomerase A

PDB DOI: https://doi.org/10.2210/pdb3KWM/pdb

Classification: ISOMERASE
Organism(s): Francisella tularensis subsp. tularensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-12-01 Released: 2010-01-05
Deposition Author(s): Orlikowska, M., Rostankowski, R., Nakka, C., Hattne, J., Grimshaw, S., Borek, D., Otwinowski, Z., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.221 (Depositor), 0.221 (DCC)
R-Value Work:
0.170 (Depositor), 0.169 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 98.82 kDa
Atom Count: 7,275
Modeled Residue Count: 871
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-5-phosphate isomerase A	A, B, C, D	224	Francisella tularensis subsp. tularensis	Mutation(s): 0 Gene Names: FTT1208, FTW_1255, rpiA EC: 5.3.1.6
UniProt
Find proteins for Q5NFM5 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NFM5 Go to UniProtKB: Q5NFM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5NFM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	I [auth C], J [auth C], K [auth C], L [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain N [auth D]	F [auth A], H [auth B], N [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain N [auth D]
3GR Query on 3GR Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	D-Glyceraldehyde C₃ H₆ O₃ MNQZXJOMYWMBOU-VKHMYHEASA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.221 (Depositor), 0.221 (DCC)
R-Value Work: 0.170 (Depositor), 0.169 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.36	α = 90
b = 73.085	β = 90
c = 75.303	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-01-05

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-01-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2020-07-08
Changes: Advisory, Atomic model, Derived calculations, Structure summary
Version 2.1: 2023-09-06
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description

3KWM | pdb_00003kwm

Crystal structure of ribose-5-isomerase A

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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