5L12 | pdb_00005l12

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase from BURKHOLDERIA PSEUDOMALLEI double mutant

PDB DOI: https://doi.org/10.2210/pdb5L12/pdb

Classification: LYASE
Organism(s): Burkholderia pseudomallei 1106a
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-07-28 Released: 2017-11-01
Deposition Author(s): Blain, J.M., Raneiri, G., Walter, R.L., Hagen, T.J., Horn, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.204 (Depositor), 0.207 (DCC)
R-Value Work:
0.165 (Depositor), 0.169 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5L12

This is version 1.1 of the entry. See complete history.

Literature

Enzyme Engineering for the Development of a High-Throughput Temperature Screen of Burkholderia pseudomallei IspF Inhibitors

Blain, J.M., Raneiri, G., Walter, R.L., Hagen, T.J., Horn, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 50.77 kDa
Atom Count: 3,682
Modeled Residue Count: 459
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	A, B, C	158	Burkholderia pseudomallei 1106a	Mutation(s): 2 Gene Names: ispF, BURPS1106A_2400 EC: 4.6.1.12
UniProt
Find proteins for A3NWD9 (Burkholderia pseudomallei (strain 1106a)) Explore A3NWD9 Go to UniProtKB: A3NWD9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3NWD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth C] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B]	D [auth A], E [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.204 (Depositor), 0.207 (DCC)
R-Value Work: 0.165 (Depositor), 0.169 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.859	α = 90
b = 68.14	β = 96.57
c = 60.408	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-11-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-11-01
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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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.