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- PDB-5cfz: Crystal structure of E. coli FabI in apo form -

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Basic information

Entry
Database: PDB / ID: 5cfz
TitleCrystal structure of E. coli FabI in apo form
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH] FabI
KeywordsOXIDOREDUCTASE / antibiotics / NAD / enoyl-ACP reductase / Oxidoreducatase
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
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 8, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,3822
Polymers65,3822
Non-polymers00
Water4,071226
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
B: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI

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


Theoretical massNumber of molelcules
Total (without water)130,7654
Polymers130,7654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area14330 Å2
ΔGint-84 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.152, 80.152, 323.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

21B-330-

HOH

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
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: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2013
RadiationMonochromator: Si(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.969→38.903 Å / Num. obs: 44807 / % possible obs: 99.4 % / Redundancy: 11.7 % / Biso Wilson estimate: 21.2 Å2 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Rsym value: 0.058 / Net I/σ(I): 26.6 / Num. measured all: 523117
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
1.969-2.089.10.16210.15613661740.0540.16210.196.2
2.08-2.212.90.1345.57840960690.0380.13415.6100
2.2-2.3512.40.1146.37117957530.0330.11417.9100
2.35-2.5412.30.0977.16597253430.0280.09721.2100
2.54-2.7812.40.0838.36160049870.0240.08325.6100
2.78-3.1111.70.069105281845200.020.06930.9100
3.11-3.5911.90.05412.54794240320.0160.05442.3100
3.59-4.411.40.041163968034760.0120.04150.5100
4.4-6.2311.40.03318.93143027660.010.03346.9100
6.23-38.90310.60.02620.51795116870.0080.02645.299.6

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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: 1QSG.pdb (model's residues were truncated to polyalanine and ligands were removed)

1qsg


Resolution: 1.97→38.9 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.219 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22505 2255 5 %RANDOM
Rwork0.19049 ---
obs0.19225 42431 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.41 Å2 / Biso mean: 21.272 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å20 Å2
2---0.24 Å20 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 1.97→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3653 0 0 226 3879
Biso mean---29.14 -
Num. residues----495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193713
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9545020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7095491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20523.947152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0515593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0741522
X-RAY DIFFRACTIONr_chiral_restr0.1470.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212804
Refine LS restraints NCS

Ens-ID: 1 / Number: 329 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.969→2.02 Å
RfactorNum. reflection% reflection
Rfree0.288 124 4.87 %
Rwork0.22 2548 -
obs--91.44 %

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