1VL1 | pdb_00001vl1

Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70A resolution

PDB DOI: https://doi.org/10.2210/pdb1VL1/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-06-30 Released: 2004-08-17
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.204 (Depositor), 0.220 (DCC)
R-Value Work:
0.165 (Depositor), 0.180 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 27.01 kDa
Atom Count: 1,949
Modeled Residue Count: 218
Deposited Residue Count: 232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconolactonase	A	232	Thermotoga maritima	Mutation(s): 0 Gene Names: PGL, DEVB, TM1154 EC: 3.1.1.31
UniProt
Find proteins for Q9X0N8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0N8 Go to UniProtKB: Q9X0N8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X0N8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT 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]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.204 (Depositor), 0.220 (DCC)
R-Value Work: 0.165 (Depositor), 0.180 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data: https://doi.org/10.18430/M31VL1

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.733	α = 90
b = 75.146	β = 90
c = 148.443	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-08-17

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-08-17
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2023-09-20
Changes: Data collection, Refinement description

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.