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- PDB-3oic: Crystal Structure of Enoyl-ACP Reductases III (FabL) from B. subt... -

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Basic information

Entry
Database: PDB / ID: 3oic
TitleCrystal Structure of Enoyl-ACP Reductases III (FabL) from B. subtilis (apo form)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADPH]
KeywordsOXIDOREDUCTASE / Fatty acid synthesis / Enoyl-ACP Reductases / FabL / Rossmann-like fold / NADPH binding
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH) / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NADP binding
Similarity search - Function
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 [NADPH] FabL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKim, K.-H. / Ha, B.H. / Kim, S.J. / Hong, S.K. / Hwang, K.Y. / Kim, E.E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structures of Enoyl-ACP Reductases I (FabI) and III (FabL) from B. subtilis
Authors: Kim, K.-H. / Ha, B.H. / Kim, S.J. / Hong, S.K. / Hwang, K.Y. / Kim, E.E.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,6593
Polymers56,5632
Non-polymers961
Water2,036113
1
A: Enoyl-[acyl-carrier-protein] reductase [NADPH]
D: Enoyl-[acyl-carrier-protein] reductase [NADPH]
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)113,3186
Polymers113,1264
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area14160 Å2
ΔGint-101 kcal/mol
Surface area38000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.211, 93.426, 66.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADPH] / Enoyl-ACP Reductases III / FabL / Enoyl-acyl carrier protein reductase III / NADPH-dependent enoyl- ...Enoyl-ACP Reductases III / FabL / Enoyl-acyl carrier protein reductase III / NADPH-dependent enoyl-ACP reductase


Mass: 28281.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: FabL / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P71079, EC: 1.3.1.10
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2M MgCl2, 0.1M imidazole, 15% Ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97787 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27593 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 49 / Num. measured all: 560220
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 3.07 / % possible all: 98.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.71 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.906 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28179 1384 5 %RANDOM
Rwork0.22561 ---
obs0.22845 26041 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.307 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.81 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 5 113 3932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223877
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.965234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4665496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.55624.731167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.28815707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9831524
X-RAY DIFFRACTIONr_chiral_restr0.1450.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022852
X-RAY DIFFRACTIONr_mcbond_it1.1221.52466
X-RAY DIFFRACTIONr_mcangle_it2.11723951
X-RAY DIFFRACTIONr_scbond_it3.32631411
X-RAY DIFFRACTIONr_scangle_it5.5514.51283
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 97 -
Rwork0.498 1787 -
obs--94.39 %

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