6OTV | pdb_00006otv

Crystal structure of putative isomerase EC2056

PDB DOI: https://doi.org/10.2210/pdb6OTV/pdb

Classification: ISOMERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-05-03 Released: 2019-05-15
Deposition Author(s): Chang, C., Evdokimova, E., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.200 (Depositor), 0.197 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6OTV

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

Literature

Crystal structure of putative isomerase EC2056

Chang, C., Evdokimova, E., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 75.8 kDa
Atom Count: 5,482
Modeled Residue Count: 700
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative isomerase YbhH	A, B	350	Escherichia coli K-12	Mutation(s): 0 Gene Names: ybhH, b0769, JW0752 EC: 5
UniProt
Find proteins for P0AAV8 (Escherichia coli (strain K12)) Explore P0AAV8 Go to UniProtKB: P0AAV8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AAV8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	I [auth A], J [auth A], T [auth B], U [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Focus chain U [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	D [auth A] E [auth A] F [auth A] K [auth A] L [auth A] D [auth A], E [auth A], F [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], S [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	C [auth A], G [auth A], H [auth A], Q [auth B], R [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.200 (Depositor), 0.197 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.416	α = 90
b = 77.416	β = 90
c = 174.266	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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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.