4DY4 | pdb_00004dy4

High resolution structure of E.coli WrbA with FMN

PDB DOI: https://doi.org/10.2210/pdb4DY4/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia coli APEC O1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-02-28 Released: 2013-03-06
Deposition Author(s): Kishko, I., Brynda, J., Kuta Smatanova, I., Ettrich, R., Carey, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.171 (Depositor), 0.171 (DCC)
R-Value Work:
0.149 (Depositor), 0.149 (DCC)
R-Value Observed:
0.150 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

High resolution structure of E.coli WrbA with FMN

Kishko, I., Brynda, J., Kuta Smatanova, I., Ettrich, R., Carey, J.

To be published.

Macromolecule Content

Total Structure Weight: 42.69 kDa
Atom Count: 3,180
Modeled Residue Count: 375
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavoprotein wrbA	A, B [auth C]	197	Escherichia coli APEC O1	Mutation(s): 0 Gene Names: wrbA, Ecok1_09050, APECO1_95 EC: 1.6.5.2
UniProt
Find proteins for A1A9Q9 (Escherichia coli O1:K1 / APEC) Explore A1A9Q9 Go to UniProtKB: A1A9Q9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1A9Q9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 F [auth C] MOL2 format, chain C [auth A] MOL2 format, chain F [auth C] mmCIF format, chain C [auth A] mmCIF format, chain F [auth C]	C [auth A], F [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth C] Interactions & Density Focus chain C [auth A] Focus chain F [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C]	D [auth A], E [auth A], G [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.171 (Depositor), 0.171 (DCC)
R-Value Work: 0.149 (Depositor), 0.149 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.15	α = 90
b = 61.15	β = 90
c = 169.59	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Kuta Smatanova, I.

Revision History (Full details and data files)

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2024-02-28
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.