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- PDB-3oje: Crystal Structure of the Bacillus cereus Enoyl-Acyl Carrier Prote... -

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Basic information

Entry
Database: PDB / ID: 3oje
TitleCrystal Structure of the Bacillus cereus Enoyl-Acyl Carrier Protein Reductase (Apo form)
ComponentsEnoyl-[acyl-carrier-protein] reductase (FabL) (NADPH)
KeywordsOXIDOREDUCTASE / Enoyl-ACP reductase / Apo form / Rossmann fold / NAD binding
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / NADP+ binding / enoyl-[acyl-carrier-protein] reductase (NADH) activity / small molecule binding / catalytic complex / identical protein binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsKim, S.J. / Ha, B.H. / Kim, K.H. / Hong, S.K. / Suh, S.W. / Kim, E.E.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Dimeric and tetrameric forms of enoyl-acyl carrier protein reductase from Bacillus cereus
Authors: Kim, S.J. / Ha, B.H. / Kim, K.H. / Hong, S.K. / Shin, K.J. / Suh, S.W. / Kim, E.E.
History
DepositionAug 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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 (FabL) (NADPH)


Theoretical massNumber of molelcules
Total (without water)27,7721
Polymers27,7721
Non-polymers00
Water1629
1
A: Enoyl-[acyl-carrier-protein] reductase (FabL) (NADPH)

A: Enoyl-[acyl-carrier-protein] reductase (FabL) (NADPH)


Theoretical massNumber of molelcules
Total (without water)55,5452
Polymers55,5452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area2800 Å2
ΔGint-14 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.148, 95.528, 67.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase (FabL) (NADPH) / Enoyl-ACP Reductase


Mass: 27772.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579/DSM31 / Gene: BC_1216 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q81GI3, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate, 8% PEG 10000, 0.4M magnesium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12174 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12174 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 5485 / % possible obs: 92.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.7 / Num. measured all: 74044
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 6.1 / % possible all: 77.1

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→24.74 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 522 9.3 %RANDOM
Rwork0.2687 ---
all-5046 --
obs-4524 80.7 %-
Solvent computationBsol: 36.6309 Å2
Displacement parametersBiso max: 131.43 Å2 / Biso mean: 76.3706 Å2 / Biso min: 38.95 Å2
Baniso -1Baniso -2Baniso -3
1--9.124 Å20 Å20 Å2
2--40.389 Å20 Å2
3----31.265 Å2
Refinement stepCycle: LAST / Resolution: 3.02→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 0 9 1706
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.553
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_scbond_it1.2992
X-RAY DIFFRACTIONc_mcangle_it2.7392
X-RAY DIFFRACTIONc_scangle_it2.2772.5
LS refinement shellResolution: 3.018→3.096 Å / Rfactor Rfree: 0.421 / Rfactor Rwork: 0.412
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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