4OMR | pdb_00004omr

Crystal structure of Tfu_1878, a putative enoyl-CoA hydratase from Thermobifida fusca YX in complex with acetoacetyl-CoA

PDB DOI: https://doi.org/10.2210/pdb4OMR/pdb

Classification: LYASE
Organism(s): Thermobifida fusca YX
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-01-27 Released: 2014-04-02
Deposition Author(s): Langner, K.M., Cooper, D.R., Chapman, H.C., Handing, K.B., 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: 1.85 Å
R-Value Free:
0.181 (Depositor), 0.193 (DCC)
R-Value Work:
0.154 (Depositor), 0.168 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of Tfu_1878, a putative enoyl-CoA hydratase from Thermobifida fusca YX in complex with acetoacetyl-CoA

Langner, K.M., Cooper, D.R., Chapman, H.C., Handing, K.B., Stead, M., Hillerich, B., Ahmed, M., Bonanno, J.B., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Macromolecule Content

Total Structure Weight: 32.97 kDa
Atom Count: 2,182
Modeled Residue Count: 255
Deposited Residue Count: 297
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	297	Thermobifida fusca YX	Mutation(s): 0 Gene Names: Tfu_1878 EC: 4.2.1.17
UniProt
Find proteins for Q47NQ8 (Thermobifida fusca (strain YX)) Explore Q47NQ8 Go to UniProtKB: Q47NQ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q47NQ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAA Query on CAA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETOACETYL-COENZYME A C₂₅ H₄₀ N₇ O₁₈ P₃ S OJFDKHTZOUZBOS-CITAKDKDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.181 (Depositor), 0.193 (DCC)
R-Value Work: 0.154 (Depositor), 0.168 (DCC)
R-Value Observed: 0.155 (Depositor)

Diffraction Data:

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.482	α = 90
b = 106.482	β = 90
c = 106.482	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2014-04-02
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 2.0: 2021-08-04
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2022-04-13
Changes: Database references, Structure summary
Version 2.2: 2024-11-20
Changes: Data collection, Structure summary