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- PDB-3gnt: Crystal Structure of the Staphylococcus aureus Enoyl-Acyl Carrier... -

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Basic information

Entry
Database: PDB / ID: 3gnt
TitleCrystal Structure of the Staphylococcus aureus Enoyl-Acyl Carrier Protein Reductase (FabI) in apo form (two molecules in AU)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Enoyl reductase / Rossmann fold
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NADP binding / 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 [NADPH] FabI
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPriyadarshi, A. / Hwang, K.Y.
CitationJournal: Proteins / Year: 2010
Title: Structural insights into Staphylococcus aureus enoyl-ACP reductase (FabI), in complex with NADP and triclosan.
Authors: Priyadarshi, A. / Kim, E.E. / Hwang, K.Y.
History
DepositionMar 18, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]


Theoretical massNumber of molelcules
Total (without water)56,0502
Polymers56,0502
Non-polymers00
Water00
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]


Theoretical massNumber of molelcules
Total (without water)112,0994
Polymers112,0994
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-20 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.099, 74.462, 70.609
Angle α, β, γ (deg.)90.00, 119.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 28024.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: fabI / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6GI75, enoyl-[acyl-carrier-protein] reductase (NADH)

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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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 400, 0.1M Tris pH 8.0, 4% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 8, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 11436 / Num. obs: 10886 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.17 / Net I/σ(I): 12.7
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.4 / Num. unique all: 635 / Rsym value: 0.17 / % possible all: 47

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PD3

2pd3


Resolution: 2.75→34.96 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.869 / SU B: 13.349 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27823 548 4.8 %RANDOM
Rwork0.24157 ---
all0.244 11436 --
obs0.24329 10886 84.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.972 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.03 Å2
2---0.14 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.75→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 0 0 3157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0460.0223194
X-RAY DIFFRACTIONr_angle_refined_deg4.261.9764302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg22.7485399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.60225.282142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg29.95915594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.3051516
X-RAY DIFFRACTIONr_chiral_restr0.7360.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022335
X-RAY DIFFRACTIONr_nbd_refined0.4350.22217
X-RAY DIFFRACTIONr_nbtor_refined0.3980.22228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2970.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4640.223
X-RAY DIFFRACTIONr_mcbond_it2.2241.52075
X-RAY DIFFRACTIONr_mcangle_it3.07323224
X-RAY DIFFRACTIONr_scbond_it5.05731272
X-RAY DIFFRACTIONr_scangle_it7.1294.51078
LS refinement shellResolution: 2.752→2.823 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 14 -
Rwork0.308 434 -
obs-635 45.21 %

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