2PPY

Crystal structure of Enoyl-CoA hydrates (gk_1992) from Geobacillus Kaustophilus HTA426

PDB DOI: https://doi.org/10.2210/pdb2PPY/pdb

Classification: LYASE
Organism(s): Geobacillus kaustophilus HTA426
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-05-01 Released: 2008-05-06
Deposition Author(s): Kanaujia, S.P., Jeyakanthan, J., Kavyashree, M., Sekar, K., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.219 (Depositor), 0.215 (DCC)
R-Value Work:
0.176 (Depositor), 0.172 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Enoyl-CoA hydrates (gk_1992) from Geobacillus Kaustophilus HTA426

Kanaujia, S.P., Jeyakanthan, J., Kavyashree, M., Sekar, K., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 180.27 kDa
Atom Count: 13,511
Modelled Residue Count: 1,577
Deposited Residue Count: 1,590
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase	A, B, C, D, E A, B, C, D, E, F	265	Geobacillus kaustophilus HTA426	Mutation(s): 0 EC: 4.2.1.17
UniProt
Find proteins for Q5KYF9 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KYF9 Go to UniProtKB: Q5KYF9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5KYF9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth F] SDF format, chain N [auth F] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F]	G [auth B] H [auth B] J [auth C] K [auth C] M [auth F] G [auth B], H [auth B], J [auth C], K [auth C], M [auth F], N [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth F] Focus chain N [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth F] Focus chain N [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D]	I [auth C], L [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain I [auth C] Focus chain L [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.219 (Depositor), 0.215 (DCC)
R-Value Work: 0.176 (Depositor), 0.172 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.201	α = 90
b = 137.345	β = 90
c = 79.131	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-05-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary