4QFE | pdb_00004qfe

Crystal Structure of an Enoyl-CoA hydratase from Mycobacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb4QFE/pdb

Classification: LYASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-20 Released: 2014-06-04
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of an Enoyl-CoA hydratase from Mycobacterium smegmatis

Dranow, D.M., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 327.99 kDa
Atom Count: 21,505
Modeled Residue Count: 2,731
Deposited Residue Count: 3,108
Unique protein chains: 1

Macromolecules

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| 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, G, H, I, J, K, L	259	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: echA5, MSMEG_1390, MSMEI_1352 EC: 4.2.1.17
UniProt
Find proteins for A0QS88 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QS88 Go to UniProtKB: A0QS88
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QS88
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain U [auth B] SDF format, chain IA [auth H] SDF format, chain FA [auth G] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth B] MOL2 format, chain IA [auth H] MOL2 format, chain FA [auth G] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth B] mmCIF format, chain IA [auth H] mmCIF format, chain FA [auth G]	FA [auth G], IA [auth H], U [auth B], Z [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain FA [auth G] Focus chain IA [auth H] Focus chain U [auth B] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth G] Focus chain IA [auth H] Focus chain U [auth B] Focus chain Z [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain ZA [auth K] SDF format, chain YA [auth K] SDF format, chain Y [auth D] SDF format, chain XA [auth K] SDF format, chain X [auth C] SDF format, chain WA [auth J] SDF format, chain W [auth C] SDF format, chain VA [auth J] SDF format, chain TA [auth J] SDF format, chain T [auth B] SDF format, chain SA [auth J] SDF format, chain S [auth B] SDF format, chain RA [auth J] SDF format, chain QA [auth J] SDF format, chain PA [auth I] SDF format, chain P [auth A] SDF format, chain OA [auth I] SDF format, chain O [auth A] SDF format, chain NA [auth I] SDF format, chain N [auth A] SDF format, chain MA [auth I] SDF format, chain M [auth A] SDF format, chain LA [auth I] SDF format, chain KA [auth I] SDF format, chain GA [auth G] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain CA [auth F] SDF format, chain BB [auth L] SDF format, chain BA [auth F] SDF format, chain AB [auth L] SDF format, chain AA [auth E] MOL2 format, chain ZA [auth K] MOL2 format, chain YA [auth K] MOL2 format, chain Y [auth D] MOL2 format, chain XA [auth K] MOL2 format, chain X [auth C] MOL2 format, chain WA [auth J] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth J] MOL2 format, chain TA [auth J] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth J] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain PA [auth I] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain KA [auth I] MOL2 format, chain GA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth F] MOL2 format, chain BB [auth L] MOL2 format, chain BA [auth F] MOL2 format, chain AB [auth L] MOL2 format, chain AA [auth E] mmCIF format, chain ZA [auth K] mmCIF format, chain YA [auth K] mmCIF format, chain Y [auth D] mmCIF format, chain XA [auth K] mmCIF format, chain X [auth C] mmCIF format, chain WA [auth J] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth J] mmCIF format, chain TA [auth J] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth J] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain PA [auth I] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth I] mmCIF format, chain KA [auth I] mmCIF format, chain GA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth F] mmCIF format, chain BB [auth L] mmCIF format, chain BA [auth F] mmCIF format, chain AB [auth L] mmCIF format, chain AA [auth E]	AA [auth E] AB [auth L] BA [auth F] BB [auth L] CA [auth F] AA [auth E], AB [auth L], BA [auth F], BB [auth L], CA [auth F], DA [auth G], EA [auth G], GA [auth G], KA [auth I], LA [auth I], M [auth A], MA [auth I], N [auth A], NA [auth I], O [auth A], OA [auth I], P [auth A], PA [auth I], QA [auth J], RA [auth J], S [auth B], SA [auth J], T [auth B], TA [auth J], VA [auth J], W [auth C], WA [auth J], X [auth C], XA [auth K], Y [auth D], YA [auth K], ZA [auth K]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain AB [auth L] Focus chain BA [auth F] Focus chain BB [auth L] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain GA [auth G] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain P [auth A] Focus chain PA [auth I] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain S [auth B] Focus chain SA [auth J] Focus chain T [auth B] Focus chain TA [auth J] Focus chain VA [auth J] Focus chain W [auth C] Focus chain WA [auth J] Focus chain X [auth C] Focus chain XA [auth K] Focus chain Y [auth D] Focus chain YA [auth K] Focus chain ZA [auth K] Interactions & Density Focus chain AA [auth E] Focus chain AB [auth L] Focus chain BA [auth F] Focus chain BB [auth L] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain GA [auth G] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain P [auth A] Focus chain PA [auth I] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain S [auth B] Focus chain SA [auth J] Focus chain T [auth B] Focus chain TA [auth J] Focus chain VA [auth J] Focus chain W [auth C] Focus chain WA [auth J] Focus chain X [auth C] Focus chain XA [auth K] Focus chain Y [auth D] Focus chain YA [auth K] Focus chain ZA [auth K]
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain JA [auth I] MOL2 format, chain R [auth B] MOL2 format, chain JA [auth I] mmCIF format, chain R [auth B] mmCIF format, chain JA [auth I]	JA [auth I], R [auth B]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain JA [auth I] Focus chain R [auth B] Interactions & Density Focus chain JA [auth I] Focus chain R [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain UA [auth J] SDF format, chain Q [auth A] SDF format, chain HA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain HA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain HA [auth G]	HA [auth G], Q [auth A], UA [auth J], V [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain HA [auth G] Focus chain Q [auth A] Focus chain UA [auth J] Focus chain V [auth B] Interactions & Density Focus chain HA [auth G] Focus chain Q [auth A] Focus chain UA [auth J] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.199 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.29	α = 84.96
b = 86.58	β = 73.62
c = 106.16	γ = 83.18

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ALS	data collection
BALBES	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-06-04

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-06-04
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description