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- PDB-4nz9: Crystal Structure of FabI from S. aureus in complex with a novel ... -

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Basic information

Entry
Database: PDB / ID: 4nz9
TitleCrystal Structure of FabI from S. aureus in complex with a novel benzimidazole inhibitor
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADPH]
Keywordsoxidoreductase/oxidoreductase inhibitor / Rossman Fold / Reductase / NADPH / Reduction / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


: / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide 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
Chem-1JT / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Enoyl-[acyl-carrier-protein] reductase [NADPH] / Enoyl-[acyl-carrier-protein] reductase [NADPH]
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMehboob, S. / Johnson, M.E. / Santarsiero, B.D.
CitationJournal: To be Published
Title: To be published
Authors: Mehboob, S. / Truong, L. / Santarsiero, B.D. / Johnson, M.E.
History
DepositionDec 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2396
Polymers61,1392
Non-polymers2,1004
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-16 kcal/mol
Surface area22910 Å2
MethodPISA
2
A: Enoyl-[acyl-carrier-protein] reductase [NADPH]
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)63,2396
Polymers61,1392
Non-polymers2,1004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3340 Å2
ΔGint-15 kcal/mol
Surface area22190 Å2
MethodPISA
3
B: Enoyl-[acyl-carrier-protein] reductase [NADPH]
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)63,2396
Polymers61,1392
Non-polymers2,1004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3410 Å2
ΔGint-13 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.545, 61.034, 112.609
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] / ENR


Mass: 30569.650 Da / Num. of mol.: 2 / Fragment: Enoyl reductase / Mutation: wild type
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / Gene: fabi, SAUSA300_0912 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q2FI66, UniProt: A0A0H2XIJ1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific)
#2: Chemical ChemComp-1JT / 1-(4-methoxy-3-methylbenzyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole


Mass: 306.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N2O
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Lithium sulfate, 40% PEG400, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.18→20 Å / Num. obs: 29318 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 12.07
Reflection shellResolution: 2.18→2.31 Å / % possible all: 93.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UIC

3uic


Resolution: 2.3→19.84 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.864 / SU B: 8.109 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27778 1265 5 %RANDOM
Rwork0.22571 ---
obs0.22829 24060 99.78 %-
all-25325 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.635 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3918 0 142 133 4193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194128
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9895591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9895507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80725.055182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34715716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0311522
X-RAY DIFFRACTIONr_chiral_restr0.0780.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023218
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 74 -
Rwork0.27 1593 -
obs--100 %

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