4LUL | pdb_00004lul

The crystal structure of the P132A, Y133D mutant of Pyrococcus furiosus phosphoglucose isomerase in complex with manganese.

PDB DOI: https://doi.org/10.2210/pdb4LUL/pdb

Classification: ISOMERASE
Organism(s): Pyrococcus furiosus DSM 3638
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-07-25 Released: 2014-07-30
Deposition Author(s): Baker, P.J., Almourfi, F.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.253 (Depositor), 0.254 (DCC)
R-Value Work:
0.196 (Depositor), 0.195 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4LUL

This is version 1.2 of the entry. See complete history.

Literature

Correlated mutation analysis as a tool for smart library design to improve protein performance.

Baker, P.J., Almourfi, F.M., Raedts, J., Joosten, H.-J., Hendriks, S., Kengen, S.W.M., Hage, W.R., Schaap, P.J., Sedelnikova, S.E., Van der Oost, J.

To be published.

Macromolecule Content

Total Structure Weight: 42.97 kDa
Atom Count: 3,143
Modeled Residue Count: 378
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate isomerase	A, B	189	Pyrococcus furiosus DSM 3638	Mutation(s): 2 Gene Names: pgiA, PF0196 EC: 5.3.1.9
UniProt
Find proteins for P83194 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P83194 Go to UniProtKB: P83194
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83194
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.253 (Depositor), 0.254 (DCC)
R-Value Work: 0.196 (Depositor), 0.195 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.3	α = 90
b = 60.03	β = 90
c = 146.67	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
xia2	data reduction
xia2	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-07-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-30
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, 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.