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

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Basic information

Entry
Database: PDB / ID: 3gns
TitleCrystal Structure of the Staphylococcus aureus Enoyl-Acyl Carrier Protein Reductase (FabI) in apo form (one molecule in AU)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Rossmann fold / Enoyl reductase
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: 2.706 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 ...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 [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3742
Polymers28,3511
Non-polymers231
Water19811
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)113,4978
Polymers113,4054
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
2
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)56,7484
Polymers56,7022
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3510 Å2
ΔGint-20 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.877, 74.716, 110.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 28351.223 Da / Num. of mol.: 1
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)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10~15% PEG 400, 0.1M Tris pH 8.3~8.5, 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
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 7634 / Num. obs: 7261 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.28 / Net I/σ(I): 19
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 2.95 / Num. unique all: 451 / Rsym value: 0.28 / % possible all: 56

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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: 2.706→37.66 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.868 / SU B: 17.01 / SU ML: 0.332 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.191 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28857 347 4.5 %RANDOM
Rwork0.21099 ---
obs0.21476 7261 91.81 %-
all-7261 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.514 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.6 Å2
Refine analyzeLuzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.706→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 1 11 1716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0480.0221720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.861.9752320
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.0365217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9525.46775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.35815316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.784158
X-RAY DIFFRACTIONr_chiral_restr0.3090.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021258
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3660.2982
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.370.21162
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2820.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1890.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4470.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.9790.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7651.51091
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.23921749
X-RAY DIFFRACTIONr_scbond_it4.5983638
X-RAY DIFFRACTIONr_scangle_it7.3194.5571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.706→2.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 15 -
Rwork0.358 297 -
obs-451 52.88 %

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