4OLQ | pdb_00004olq

Crystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium

PDB DOI: https://doi.org/10.2210/pdb4OLQ/pdb

Classification: LYASE
Organism(s): Hyphomonas neptunium ATCC 15444
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-01-24 Released: 2014-03-12
Deposition Author(s): Szlachta, K., Cooper, D.R., Chapman, H.C., Cymborowski, M.T., Stead, M., Hillerich, B., Ahmed, M., Bonanno, J.B., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.261 (Depositor), 0.260 (DCC)
R-Value Work:
0.230 (Depositor), 0.228 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium

Szlachta, K., Cooper, D.R., Chapman, H.C., Cymborowski, M.T., Stead, M., Hillerich, B., Ahmed, M., Bonanno, J.B., Seidel, R., Almo, S.C., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 182.59 kDa
Atom Count: 11,585
Modeled Residue Count: 1,597
Deposited Residue Count: 1,692
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase family protein	A, B, C, D, E A, B, C, D, E, F	282	Hyphomonas neptunium ATCC 15444	Mutation(s): 0 Gene Names: HNE_1107 EC: 4.2.1.17
UniProt
Find proteins for Q0C365 (Hyphomonas neptunium (strain ATCC 15444)) Explore Q0C365 Go to UniProtKB: Q0C365
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0C365
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain R [auth F] MOL2 format, chain J [auth C] MOL2 format, chain R [auth F] mmCIF format, chain J [auth C] mmCIF format, chain R [auth F]	J [auth C], R [auth F]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain R [auth F] Interactions & Density Focus chain J [auth C] Focus chain R [auth F]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain S [auth F] MOL2 format, chain K [auth C] MOL2 format, chain S [auth F] mmCIF format, chain K [auth C] mmCIF format, chain S [auth F]	K [auth C], S [auth F]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain S [auth F] Interactions & Density Focus chain K [auth C] Focus chain S [auth F]
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth E] MOL2 format, chain P [auth E] mmCIF format, chain P [auth E]	P [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth E] Interactions & Density Focus chain P [auth E]
UNL Query on UNL Download:Ideal Coordinates CCD File	G [auth A] I [auth B] L [auth C] M [auth D] N [auth D] G [auth A], I [auth B], L [auth C], M [auth D], N [auth D], O [auth D], Q [auth E], T [auth F]	Unknown ligand MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth E] Focus chain T [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth E] Focus chain T [auth F]

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: 2.70 Å
R-Value Free: 0.261 (Depositor), 0.260 (DCC)
R-Value Work: 0.230 (Depositor), 0.228 (DCC)
R-Value Observed: 0.232 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.595	α = 90
b = 122.39	β = 90
c = 210.232	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MD2	data collection
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-03-12

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2014-03-12
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-27
Changes: Data collection, Refinement description, Structure summary