4NEK

Putative enoyl-CoA hydratase/carnithine racemase from Magnetospirillum magneticum AMB-1

PDB DOI: https://doi.org/10.2210/pdb4NEK/pdb

Classification: ISOMERASE
Organism(s): Paramagnetospirillum magneticum AMB-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-29 Released: 2013-11-27
Deposition Author(s): Tkaczuk, K.L., Cooper, D.R., Geffken, K., Chapman, H.C., 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: 2.30 Å
R-Value Free: 0.207
R-Value Work: 0.176
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

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

Literature

Putative enoyl-CoA hydratase/carnithine racemase from Magnetospirillum magneticum AMB-1

Tkaczuk, K.L., Cooper, D.R., Geffken, K., Chapman, H.C., 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: 163.65 kDa
Atom Count: 11,590
Modelled Residue Count: 1,508
Deposited Residue Count: 1,512
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/carnithine racemase	A, B, C, D, E A, B, C, D, E, F	252	Paramagnetospirillum magneticum AMB-1	Mutation(s): 0 Gene Names: amb4133
UniProt
Find proteins for Q2VZN8 (Magnetospirillum magneticum (strain AMB-1 / ATCC 700264)) Explore Q2VZN8 Go to UniProtKB: Q2VZN8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2VZN8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 A] SDF format, chain H [auth B] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth F]	G [auth A], H [auth B], I [auth D], J [auth D], K [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [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: 2.30 Å
R-Value Free: 0.207
R-Value Work: 0.176
R-Value Observed: 0.178
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M3BC7G

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.285	α = 90
b = 156.683	β = 113.81
c = 79.297	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-11-27

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-11-27
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary

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4NEK

Putative enoyl-CoA hydratase/carnithine racemase from Magnetospirillum magneticum AMB-1

Putative enoyl-CoA hydratase/carnithine racemase from Magnetospirillum magneticum AMB-1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)