5VE2 | pdb_00005ve2

Crystal structure of enoyl-CoA hydratase/isomerase from Pseudoalteromonas atlantica T6c at 2.3 A resolution.

PDB DOI: https://doi.org/10.2210/pdb5VE2/pdb

Classification: ISOMERASE,LYASE
Organism(s): Paraglaciecola sp. T6c
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-03 Released: 2017-04-19
Deposition Author(s): Siuda, M.K., Shabalin, I.G., Cooper, D.R., Chapman, H.C., Tkaczuk, K.L., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.258 (Depositor), 0.264 (DCC)
R-Value Work:
0.205 (Depositor), 0.218 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of enoyl-CoA hydratase/isomerase from Pseudoalteromonas atlantica T6c at 2.3 A resolution.

Siuda, M.K., Shabalin, I.G., Cooper, D.R., Almo, S.C., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 364.88 kDa
Atom Count: 24,561
Modeled Residue Count: 3,009
Deposited Residue Count: 3,300
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	275	Paraglaciecola sp. T6c	Mutation(s): 0 Gene Names: Patl_1462 EC: 4.2.1.17

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D]	P [auth C], R [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Focus chain R [auth D] Interactions & Density Focus chain P [auth C] Focus chain R [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	X [auth G], Z [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain X [auth G] Focus chain Z [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E]	S [auth E], T [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain S [auth E] Focus chain T [auth E] Interactions & Density Focus chain S [auth E] Focus chain T [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain CA [auth K] SDF format, chain DA [auth L] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain BA [auth J] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain BA [auth J] mmCIF format, chain AA [auth I] mmCIF format, chain CA [auth K] mmCIF format, chain DA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Y [auth H] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain BA [auth J]	AA [auth I] BA [auth J] CA [auth K] DA [auth L] M [auth A] AA [auth I], BA [auth J], CA [auth K], DA [auth L], M [auth A], N [auth B], O [auth C], Q [auth D], U [auth E], V [auth F], W [auth G], Y [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain Y [auth H]

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, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.258 (Depositor), 0.264 (DCC)
R-Value Work: 0.205 (Depositor), 0.218 (DCC)
R-Value Observed: 0.208 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.66	α = 90
b = 160.141	β = 90.12
c = 136.271	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
HKL-3000	data scaling
SHELXD	phasing
DM	phasing
MLPHARE	phasing
HKL-3000	phasing
BUCCANEER	model building
REFMAC	refinement
HKL-3000	data reduction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-04-19

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2017-04-19
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Refinement description
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary