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- PDB-5cg2: Crystal structure of E. coli FabI bound to the thiocarbamoylated ... -

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Basic information

Entry
Database: PDB / ID: 5cg2
TitleCrystal structure of E. coli FabI bound to the thiocarbamoylated benzodiazaborine inhibitor 35b.
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-CJ3 / 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: 2.11 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)67,1196
Polymers65,3822
Non-polymers1,7374
Water3,837213
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)134,23812
Polymers130,7654
Non-polymers3,4748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area18570 Å2
ΔGint-102 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.913, 79.913, 323.789
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-CJ3 / 1-hydroxy-2,3,1-benzodiazaborinine-2(1H)-carbothioamide


Mass: 205.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H8BN3OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
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: 2.11→69.21 Å / Num. all: 36240 / Num. obs: 36240 / % possible obs: 99.3 % / Redundancy: 17.2 % / Rpim(I) all: 0.012 / Rrim(I) all: 0.049 / Rsym value: 0.048 / Net I/av σ(I): 10.4 / Net I/σ(I): 42.6 / Num. measured all: 624835
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.11-2.23140.1156.36902249210.030.11518.195
2.23-2.3617.40.1245.58530249140.0320.12424.4100
2.36-2.5219.10.0729.98845746350.0170.07232.6100
2.52-2.7318.80.06211.38149543380.0150.06239.1100
2.73-2.9918.70.05512.57520640190.0130.05546100
2.99-3.3417.40.04713.96430536920.0110.04755100
3.34-3.8517.20.04513.75622032630.0110.04561.9100
3.85-4.7216.60.03815.44686928260.0090.03867.8100
4.72-6.6816.40.03715.93697122610.0090.03764.1100
6.68-39.65615.30.03216.22098813710.0080.03264.599.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CFZ

5cfz


Resolution: 2.11→69.21 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.117 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 1836 5.1 %RANDOM
Rwork0.2019 ---
obs0.2039 34171 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.01 Å2 / Biso mean: 24.417 Å2 / Biso min: 9.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.11→69.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 116 213 3839
Biso mean--30.82 31.23 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193696
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9565024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4425474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23624.167144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57415561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4091519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213001
Refine LS restraints NCS

Ens-ID: 1 / Number: 308 / 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: 2.111→2.166 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 111 -
Rwork0.197 1986 -
all-2097 -
obs--88.37 %

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