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

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Basic information

Entry
Database: PDB / ID: 3oid
TitleCrystal Structure of Enoyl-ACP Reductases III (FabL) from B. subtilis (complex with NADP and TCL)
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) / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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
Chem-NDP / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADPH] FabL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,26612
Polymers113,1264
Non-polymers4,1408
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-100 kcal/mol
Surface area34740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.376, 110.683, 85.169
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28281.445 Da / Num. of mol.: 4
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): BL21 (DE3) / References: UniProt: P71079, EC: 1.3.1.10
#2: Chemical
ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6M sodium citrate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 100171 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 34.7 / Num. measured all: 1861429
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 8.95 / % possible all: 94.9

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Processing

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

3oic


Resolution: 1.8→36.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.797 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18061 4965 5 %RANDOM
Rwork0.1493 ---
obs0.15086 94292 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.994 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.16 Å2
2---0.2 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7579 0 260 545 8384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0227947
X-RAY DIFFRACTIONr_angle_refined_deg2.1382.00810770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1224.984319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.589151417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3941548
X-RAY DIFFRACTIONr_chiral_restr0.1930.21260
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025752
X-RAY DIFFRACTIONr_mcbond_it1.3271.54920
X-RAY DIFFRACTIONr_mcangle_it2.31927888
X-RAY DIFFRACTIONr_scbond_it3.99233027
X-RAY DIFFRACTIONr_scangle_it6.5414.52882
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 357 -
Rwork0.173 6540 -
obs--92.66 %

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