6OZ7

Putative oxidoreductase from Escherichia coli str. K-12

PDB DOI: https://doi.org/10.2210/pdb6OZ7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-05-15 Released: 2019-05-29
Deposition Author(s): Osipiuk, J., Skarina, T., Mesa, N., Endres, M., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.169
R-Value Work: 0.123
R-Value Observed: 0.126

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Putative oxidoreductase from Escherichia coli str. K-12

Osipiuk, J., Skarina, T., Mesa, N., Endres, M., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 217.19 kDa
Atom Count: 16,852
Modelled Residue Count: 1,912
Deposited Residue Count: 2,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized oxidoreductase YohF	A, B, C, D, E A, B, C, D, E, F, G, H	254	Escherichia coli K-12	Mutation(s): 0 Gene Names: yohF, yohE, b2137, JW2125 EC: 1
UniProt
Find proteins for P33368 (Escherichia coli (strain K12)) Explore P33368 Go to UniProtKB: P33368
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33368
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	L [auth C], N [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain L [auth C] Focus chain N [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain T [auth H] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth H] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth H]	P [auth E], Q [auth E], T [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain P [auth E] Focus chain Q [auth E] Focus chain T [auth H] Interactions & Density Focus chain P [auth E] Focus chain Q [auth E] Focus chain T [auth H]
CA Query on CA 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 M [auth D] SDF format, chain O [auth E] SDF format, chain R [auth F] SDF format, chain S [auth G] SDF format, chain U [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth G] MOL2 format, chain U [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth G] mmCIF format, chain U [auth H]	I [auth A] J [auth B] K [auth C] M [auth D] O [auth E] I [auth A], J [auth B], K [auth C], M [auth D], O [auth E], R [auth F], S [auth G], U [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain U [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain U [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.169
R-Value Work: 0.123
R-Value Observed: 0.126
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/m36oz7

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.819	α = 82.59
b = 72.21	β = 87.03
c = 119.945	γ = 67.82

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-29

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2019-05-29
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description