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- PDB-5cg1: Crystal structure of E. coli FabI bound to the carbamoylated benz... -

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Basic information

Entry
Database: PDB / ID: 5cg1
TitleCrystal structure of E. coli FabI bound to the carbamoylated benzodiazaborine inhibitor 14b.
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH] FabI
KeywordsOxidoreductase/Oxidoreductase Inhibitor / antibiotics / NAD / enoyl-ACP reductase / Oxidoreducatase-Oxidoreducatase Inhibitor complex / Oxidoreductase-Oxidoreductase Inhibitor complex
Function / homology
Function and homology information


NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex ...NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex / identical protein binding / membrane / cytosol
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-BBN / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsJordan, C.A. / Vey, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
CSUN Faculty DevelopmentProbationary Faculty Support Grant United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Crystallographic insights into the structure-activity relationships of diazaborine enoyl-ACP reductase inhibitors.
Authors: Jordan, C.A. / Sandoval, B.A. / Serobyan, M.V. / Gilling, D.H. / Groziak, M.P. / Xu, H.H. / Vey, J.L.
History
DepositionJul 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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] FabI
B: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0876
Polymers65,3822
Non-polymers1,7054
Water6,539363
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
B: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)134,17412
Polymers130,7654
Non-polymers3,4108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area18860 Å2
ΔGint-108 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.070, 80.070, 325.016
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 2 - 257 / Label seq-ID: 45 - 300

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] FabI / ENR / NADH-dependent enoyl-ACP reductase


Mass: 32691.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fabI, envM, b1288, JW1281 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AEK4, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-BBN / 1-hydroxy-2,3,1-benzodiazaborinine-2(1H)-carboxamide


Mass: 188.979 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8BN3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M citrate pH 7.0, 0.1M ammonium sulfate, 22%w/v PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2014
RadiationMonochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.07→69.41 Å / Num. obs: 38218 / % possible obs: 98.1 % / Redundancy: 9 % / Biso Wilson estimate: 21.8 Å2 / Rsym value: 0.053 / Net I/σ(I): 27.4
Reflection shellResolution: 2.07→2.18 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 13.5 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CFZ

5cfz


Resolution: 2.07→69.41 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.122 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1944 5.1 %RANDOM
Rwork0.2044 ---
obs0.2066 35992 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.36 Å2 / Biso mean: 21.14 Å2 / Biso min: 7.29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.07→69.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 116 363 4122
Biso mean--29.93 31 -
Num. residues----495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193832
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9515206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3935491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68624.067150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63515586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7341520
X-RAY DIFFRACTIONr_chiral_restr0.0990.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213109
Refine LS restraints NCS

Ens-ID: 1 / Number: 326 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.069→2.122 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 105 -
Rwork0.225 1834 -
all-1939 -
obs--74.72 %

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