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- PDB-5gvh: Structure of FabK from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 5gvh
TitleStructure of FabK from Thermotoga maritima
ComponentsEnoyl-[acyl-carrier-protein] reductase [FMN]
KeywordsOXIDOREDUCTASE / FabK / Enoyl-ACP reductase II
Function / homology
Function and homology information


nitronate monooxygenase activity / enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / nucleotide binding
Similarity search - Function
Enoyl-(acyl-carrier-protein) reductase II, putative / Nitronate monooxygenase / Nitronate monooxygenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [FMN] / Enoyl-[acyl-carrier-protein] reductase [FMN]
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.294 Å
AuthorsKim, E.E. / Shin, S.C. / Ha, B.H. / Moon, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
NRF 20110021713 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural and biochemical characterization of FabK from Thermotoga maritima.
Authors: Ha, B.H. / Shin, S.C. / Moon, J.H. / Keum, G. / Kim, C.W. / Kim, E.E.
History
DepositionSep 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [FMN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1943
Polymers33,7151
Non-polymers4792
Water1,09961
1
A: Enoyl-[acyl-carrier-protein] reductase [FMN]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [FMN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3896
Polymers67,4302
Non-polymers9594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area6450 Å2
ΔGint-63 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.611, 77.107, 59.085
Angle α, β, γ (deg.)90.000, 99.940, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [FMN] / Uncharacterized protein


Mass: 33715.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0800, Tmari_0801 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZQ7, UniProt: R4NR95*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Bicine, pH 9.0, 1.5 M LiCl, 23% PEG 6000 / PH range: 8.5-9.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9789, 0.9792, 0.9814
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 21, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97921
30.98141
ReflectionResolution: 2.29→40.5 Å / Num. obs: 22681 / % possible obs: 94.5 % / Redundancy: 6.8 % / Net I/σ(I): 34.5
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.294→40.453 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.53 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 550 10.05 %
Rwork0.1932 --
obs0.197 22681 88.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.1 Å2 / Biso mean: 41.6272 Å2 / Biso min: 14.93 Å2
Refinement stepCycle: final / Resolution: 2.294→40.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 32 61 2426
Biso mean--34.02 38.14 -
Num. residues----311

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