3F4W | pdb_00003f4w

The 1.65A Crystal Structure of 3-hexulose-6-phosphate synthase from Salmonella typhimurium

PDB DOI: https://doi.org/10.2210/pdb3F4W/pdb

Classification: SYNTHASE, LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-03 Released: 2008-11-25
Deposition Author(s): Vijayalakshmi, J., Woodard, R.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.250 (Depositor), 0.243 (DCC)
R-Value Work:
0.213 (Depositor), 0.205 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The 1.65A Crystal Structure of 3-hexulose-6-phosphate synthase from Salmonella typhimurium

Vijayalakshmi, J., Meredith, T.C., Woodard, R.W.

To be published.

Macromolecule Content

Total Structure Weight: 45.69 kDa
Atom Count: 3,694
Modeled Residue Count: 422
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hexulose 6 phosphate synthase	A, B	211	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: HUMPS, STM2755 EC: 4.1.2 (PDB Primary Data), 4.1.2.43 (UniProt), 4.1.1.85 (UniProt)
UniProt
Find proteins for Q8ZMP9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZMP9 Go to UniProtKB: Q8ZMP9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZMP9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		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: 1.65 Å
R-Value Free: 0.250 (Depositor), 0.243 (DCC)
R-Value Work: 0.213 (Depositor), 0.205 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.971	α = 90
b = 108.971	β = 90
c = 36.702	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

Vijayalakshmi, J.

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
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.