4Q51

Crystal structure of a putative molybdenum cofactor biosynthesis protein F from Burkholderia cenocepacia J2315

PDB DOI: https://doi.org/10.2210/pdb4Q51/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-04-15 Released: 2014-05-07
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Kiryukhina, O., Minasov, G., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.209
R-Value Work: 0.160
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative molybdenum cofactor biosynthesis protein F from Burkholderia cenocepacia J2315

Filippova, E.V., Wawrzak, Z., Kiryukhina, O., Minasov, G., Jedrzejczak, R., Joachimiak, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 62.56 kDa
Atom Count: 4,598
Modelled Residue Count: 529
Deposited Residue Count: 562
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	281	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAM2002
UniProt
Find proteins for B4EN46 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EN46 Go to UniProtKB: B4EN46
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EN46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA 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]	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.209
R-Value Work: 0.160
R-Value Observed: 0.163
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.402	α = 90
b = 46.163	β = 99.14
c = 77.293	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Filippova, E.V.

Jedrzejczak, R.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 1.1: 2014-08-13
Changes: Database references, Structure summary
Version 1.2: 2017-11-22
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.