1OV8 | pdb_00001ov8

Auracyanin B structure in space group, P65

PDB DOI: https://doi.org/10.2210/pdb1OV8/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Chloroflexus aurantiacus
Mutation(s): No

Deposited: 2003-03-25 Released: 2003-09-09
Deposition Author(s): Lee, M., Maher, M.J., Freeman, H.C., Guss, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.192 (Depositor), 0.200 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Auracyanin B structure in space group P6(5).

Lee, M., Maher, M.J., Freeman, H.C., Guss, J.M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1545-1550

PubMed: 12925783 Search on PubMed
DOI: https://doi.org/10.1107/s0907444903014161
Primary Citation of Related Structures:
1OV8

PubMed Abstract:
The structure of auracyanin B, a 'blue' copper protein produced by Chloroflexus aurantiacus, has previously been solved and refined in the hexagonal space group P6(4)22 with a single molecule in the asymmetric unit. The protein has now been crystallized in space group P6(5), with unit-cell parameters a = b = 115.9, c = 108.2 A. In the new crystal form, the asymmetric unit contains four protein molecules. The structure has been solved by molecular replacement and refined at 1.9 A resolution. The final residuals are R = 19.2% and R(free) = 21.9%. In relation to the earlier crystal structure, the doubling of the unit-cell volume and the lower symmetry are explained by small rotations of the molecules with respect to one another.

Organizational Affiliation

School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.

Macromolecule Content

Total Structure Weight: 58.45 kDa
Atom Count: 4,642
Modelled Residue Count: 556
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Auracyanin B	A, B, C, D	140	Chloroflexus aurantiacus	Mutation(s): 0
UniProt
Find proteins for P27197 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore P27197 Go to UniProtKB: P27197
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27197
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain O [auth D]	G [auth A], I [auth B], J [auth B], M [auth C], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C]	F [auth A], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.219 (Depositor), 0.220 (DCC)
R-Value Work: 0.192 (Depositor), 0.200 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.885	α = 90
b = 115.885	β = 90
c = 108.149	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-09-09
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.3: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description