5F12

WrbA in complex with FMN under crystallization conditions of WrbA-FMN-BQ structure (4YQE)

PDB DOI: https://doi.org/10.2210/pdb5F12/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-11-29 Released: 2016-05-25
Deposition Author(s): Degtjarik, O., Brynda, J., Ettrichova, O., Kuta Smatanova, I., Carey, J., Ettrich, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.205
R-Value Work: 0.178
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA.

Degtjarik, O., Brynda, J., Ettrichova, O., Kuty, M., Sinha, D., Kuta Smatanova, I., Carey, J., Ettrich, R., Reha, D.

(2016) J Phys Chem B 120: 4867-4877

PubMed: 27183467 Search on PubMed
DOI: https://doi.org/10.1021/acs.jpcb.5b11958
Primary Citation of Related Structures:
4YQE, 5F12

PubMed Abstract:
Quantum mechanical calculations using the Marcus equation are applied to compare the electron-transfer probability for two distinct crystal structures of the Escherichia coli protein WrbA, an FMN-dependent

Organizational Affiliation

Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.

Macromolecule Content

Total Structure Weight: 42.41 kDa
Atom Count: 3,115
Modelled Residue Count: 381
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H dehydrogenase (quinone)	A, B	197	Escherichia coli K-12	Mutation(s): 0 Gene Names: wrbA, b1004, JW0989 EC: 1.6.5.2
UniProt
Find proteins for P0A8G6 (Escherichia coli (strain K12)) Explore P0A8G6 Go to UniProtKB: P0A8G6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A8G6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN 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]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-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
MHO Query on MHO	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.205
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.75	α = 90
b = 60.75	β = 90
c = 169.02	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
BALBES	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-05-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-05-25
Type: Initial release
Version 1.1: 2016-06-01
Changes: Database references
Version 1.2: 2016-06-08
Changes: Database references
Version 1.3: 2016-06-22
Changes: Database references
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Refinement description