2W8H | pdb_00002w8h

Crystal structure of spin labeled Wza24-345.

PDB DOI: https://doi.org/10.2210/pdb2W8H/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2009-01-16 Released: 2009-02-10
Deposition Author(s): Hagelueken, G., Ingledew, W.J., Huang, H., Petrovic-Stojanovska, B., Whitfield, C., ElMkami, H., Schiemann, O., Naismith, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free:
0.229 (Depositor), 0.193 (DCC)
R-Value Work:
0.211 (Depositor)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Peldor Distance Fingerprinting of the Octameric Outer-Membrane Protein Wza from Escherichia Coli.

Hagelueken, G., Ingledew, W.J., Huang, H., Petrovic-Stojanovska, B., Whitfield, C., Elmkami, H., Schiemann, O., Naismith, J.H.

(2009) Angew Chem Int Ed Engl 48: 2904

PubMed: 19294709 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.200805758
Primary Citation Related Structures:
2W8H, 2W8I

PubMed Abstract:
Distance fingerprinting: Pulsed electron-electron double resonance spectroscopy (PELDOR) is applied to the octameric membrane protein complex Wza of E. coli. The data yielded a detailed distance fingerprint of its periplasmic region that compares favorably to the crystal structure. These results provide the foundation to study conformation changes from interaction with partner proteins.

Organizational Affiliation

Centre for Biomolecular Sciences, The University of St. Andrews, Fife KY16 9RH, UK.

Macromolecule Content

Total Structure Weight: 289.08 kDa
Atom Count: 19,998
Modeled Residue Count: 2,576
Deposited Residue Count: 2,632
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE OUTER MEMBRANE LIPOPROTEIN WZA	A, B, C, D, E A, B, C, D, E, F, G, H	329	Escherichia coli	Mutation(s): 1 Membrane Entity: Yes
UniProt
Find proteins for Q9X4B7 (Escherichia coli) Explore Q9X4B7 Go to UniProtKB: Q9X4B7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X4B7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTN Query on MTN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth G] SDF format, chain Q [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth H]	I [auth A] J [auth B] K [auth C] L [auth D] N [auth E] I [auth A], J [auth B], K [auth C], L [auth D], N [auth E], O [auth F], P [auth G], Q [auth H]	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate C₁₀ H₁₈ N O₃ S₂ MXZPGYFBZHBAQM-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.229 (Depositor), 0.193 (DCC)
R-Value Work: 0.211 (Depositor)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.153	α = 90
b = 141.152	β = 90
c = 167.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-02-10

Deposition Author(s):

Hagelueken, G.

Ingledew, W.J.

Huang, H.

Petrovic-Stojanovska, B.

Revision History (Full details and data files)

Version 1.0: 2009-02-10
Type: Initial release
Version 1.1: 2011-05-12
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary