2QLA

Crystal Structure of a 16-Helix Bundle Architecture Produced by the Zinc-Mediated Self Assembly of Four Cytochrome cb562 Molecules

PDB DOI: https://doi.org/10.2210/pdb2QLA/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-07-12 Released: 2007-11-06
Deposition Author(s): Tezcan, F.A., Salgado, E.N., Faraone-Mennella, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.295
R-Value Work: 0.248
R-Value Observed: 0.248

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Controlling protein-protein interactions through metal coordination: assembly of a 16-helix bundle protein.

Salgado, E.N., Faraone-Mennella, J., Tezcan, F.A.

(2007) J Am Chem Soc 129: 13374-13375

PubMed: 17929927 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/ja075261o
Primary Citation of Related Structures:
2QLA

Organizational Affiliation

Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Macromolecule Content

Total Structure Weight: 49.63 kDa
Atom Count: 3,483
Modelled Residue Count: 424
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A, B, C, D	106	Escherichia coli	Mutation(s): 5 Gene Names: cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.295
R-Value Work: 0.248
R-Value Observed: 0.248
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.984	α = 90
b = 66.659	β = 90
c = 68.901	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
APEX	data collection
SAINT	data reduction
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-11-06

Deposition Author(s):

Tezcan, F.A.

Salgado, E.N.

Faraone-Mennella, J.

Revision History (Full details and data files)

Version 1.0: 2007-11-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-18
Changes: Advisory, Refinement description
Version 1.3: 2018-03-07
Changes: Data collection
Version 1.4: 2021-10-20
Changes: Advisory, Database references, Derived calculations
Version 1.5: 2023-08-30
Changes: Data collection, Refinement description

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Help and Resources

2QLA

Crystal Structure of a 16-Helix Bundle Architecture Produced by the Zinc-Mediated Self Assembly of Four Cytochrome cb562 Molecules

Controlling protein-protein interactions through metal coordination: assembly of a 16-helix bundle protein.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)