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), 0.217 (DCC)
R-Value Work:
0.165 (Depositor), 0.177 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.217 (DCC)
R-Value Work: 0.165 (Depositor), 0.177 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data:

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

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View more in-depth experimental data

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

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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.