2JCB | pdb_00002jcb

The crystal structure of 5-formyl-tetrahydrofolate cycloligase from Bacillus anthracis (BA4489)

PDB DOI: https://doi.org/10.2210/pdb2JCB/pdb

Classification: LIGASE
Organism(s): Bacillus anthracis str. Ames
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-12-21 Released: 2007-02-20
Deposition Author(s): Meier, C., Carter, L.G., Winter, G., Owens, R.J., Stuart, D.I., Esnouf, R.M., Oxford Protein Production Facility (OPPF), Structural Proteomics in Europe (SPINE)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.238 (Depositor), 0.233 (DCC)
R-Value Work:
0.189 (Depositor), 0.185 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of 5-Formyltetrahydrofolate Cyclo-Ligase from Bacillus Anthracis (Ba4489).

Meier, C., Carter, L.G., Winter, G., Owens, R.J., Stuart, D.I., Esnouf, R.M.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 168

PubMed: 17329806 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309107007221
Primary Citation Related Structures:
2JCB

PubMed Abstract:
Bacillus anthracis is a spore-forming bacterium and the causative agent of the disease anthrax. The Oxford Protein Production Facility has been targeting proteins from B. anthracis in order to develop high-throughput technologies within the Structural Proteomics in Europe project. As part of this work, the structure of 5-formyltetrahydrofolate cyclo-ligase (BA4489) has been determined by X-ray crystallography to 1.6 A resolution. The structure, solved in complex with magnesium-ion-bound ADP and phosphate, gives a detailed picture of the proposed catalytic mechanism of the enzyme. Chemical differences from other cyclo-ligase structures close to the active site that could be exploited to design specific inhibitors are also highlighted.

Organizational Affiliation

Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England.

Macromolecule Content

Total Structure Weight: 47.94 kDa
Atom Count: 3,558
Modeled Residue Count: 384
Deposited Residue Count: 400
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE FAMILY PROTEIN	A, B	200	Bacillus anthracis str. Ames	Mutation(s): 0 EC: 6.3.3.2
UniProt
Find proteins for A0A6L8PZ12 (Bacillus anthracis) Explore A0A6L8PZ12 Go to UniProtKB: A0A6L8PZ12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L8PZ12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.238 (Depositor), 0.233 (DCC)
R-Value Work: 0.189 (Depositor), 0.185 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.152	α = 74.92
b = 45.499	β = 78.01
c = 66.999	γ = 70.14

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-02-20

Deposition Author(s):

Oxford Protein Production Facility (OPPF)

Structural Proteomics in Europe (SPINE)

Revision History (Full details and data files)

Version 1.0: 2007-02-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2015-05-06
Changes: Source and taxonomy
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description