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- PDB-3oig: Crystal Structure of Enoyl-ACP Reductases I (FabI) from B. subtil... -

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Basic information

Entry
Database: PDB / ID: 3oig
TitleCrystal Structure of Enoyl-ACP Reductases I (FabI) from B. subtilis (complex with NAD and INH)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Fatty acid synthesis / Rossmann-like fold / Enoyl-ACP Reductases / NADH binding / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / cellular response to cold
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
Chem-IMJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0293
Polymers28,9771
Non-polymers1,0522
Water4,774265
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)120,11512
Polymers115,9084
Non-polymers4,2088
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_547x,-y-1,-z+21
Buried area15550 Å2
ΔGint-64 kcal/mol
Surface area35880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.126, 80.004, 88.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP Reductases I / FabI / NADH-dependent enoyl-ACP reductase / Cold shock-induced protein 15 ...Enoyl-ACP Reductases I / FabI / NADH-dependent enoyl-ACP reductase / Cold shock-induced protein 15 / CSI15 / Vegetative protein 241 / VEG241


Mass: 28976.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: FabI / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P54616, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-IMJ / (2E)-N-[(1,2-dimethyl-1H-indol-3-yl)methyl]-N-methyl-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)prop-2-enamide


Mass: 388.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M di-ammonium tartrate, 22% (w/v) PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12174 Å
DetectorType: Bruker Proteum 300 / Detector: CCD / Date: Nov 15, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12174 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 67984 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 19.8 / Num. measured all: 672557
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.93

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CNSrefinement
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OIF

3oif


Resolution: 1.25→33.69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.56 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1848 3438 5.1 %RANDOM
Rwork0.16656 ---
obs0.16749 64281 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.324 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.25→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 73 265 2310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0212082
X-RAY DIFFRACTIONr_angle_refined_deg2.4612.0042827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.52723.83786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6315345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5421515
X-RAY DIFFRACTIONr_chiral_restr0.170.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021552
X-RAY DIFFRACTIONr_mcbond_it1.3331.51284
X-RAY DIFFRACTIONr_mcangle_it2.24922059
X-RAY DIFFRACTIONr_scbond_it3.4383798
X-RAY DIFFRACTIONr_scangle_it5.4454.5768
LS refinement shellResolution: 1.247→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 242 -
Rwork0.23 4596 -
obs--96.92 %

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