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- PDB-3nrc: Crystal Structure of the Francisella tularensis enoyl-acyl carrie... -

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Basic information

Entry
Database: PDB / ID: 3nrc
TitleCrystal Structure of the Francisella tularensis enoyl-acyl carrier protein reductase (FabI) in complex with NAD+ and triclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase (NADH)
KeywordsOXIDOREDUCTASE / Rossmann fold / enoyl-acyl carrier protein reductase / NADH binding
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsMehboob, S. / Santarsiero, B.D. / Truong, K. / Johnson, M.E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of the Francisella tularensis enoyl-acyl carrier protein reductase (FabI) in complex with NAD(+) and triclosan.
Authors: Mehboob, S. / Truong, K. / Santarsiero, B.D. / Johnson, M.E.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Dec 28, 2016Group: Structure summary
Revision 1.4Sep 6, 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

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase (NADH)
B: Enoyl-[acyl-carrier-protein] reductase (NADH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9196
Polymers60,0132
Non-polymers1,9064
Water2,558142
1
A: Enoyl-[acyl-carrier-protein] reductase (NADH)
B: Enoyl-[acyl-carrier-protein] reductase (NADH)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)123,83812
Polymers120,0264
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area21880 Å2
ΔGint-217 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.080, 85.120, 51.760
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 (NADH)


Mass: 30006.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: Schu4 / Gene: fabI, fabI gene, FTT_0782 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5NGQ3, 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-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Comment: antifungal, antibiotic, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 2M Ammonium sulfate, 0.1M phosphate-citrate buffer pH4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→70 Å / Num. all: 36922 / Num. obs: 31040 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9 % / Rmerge(I) obs: 0.17 / Rsym value: 0.15 / Net I/σ(I): 16.03

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JJY

2jjy


Resolution: 2.101→19.806 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 28.15 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2424 1560 5.04 %
Rwork0.1864 --
obs0.1892 30957 95.35 %
all-32243 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.597 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.0816 Å2-0 Å20 Å2
2---15.8273 Å20 Å2
3---30.9089 Å2
Refinement stepCycle: LAST / Resolution: 2.101→19.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 122 142 4090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074028
X-RAY DIFFRACTIONf_angle_d1.0625456
X-RAY DIFFRACTIONf_dihedral_angle_d15.0021458
X-RAY DIFFRACTIONf_chiral_restr0.076624
X-RAY DIFFRACTIONf_plane_restr0.003682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.101-2.16870.3376570.30461418X-RAY DIFFRACTION50
2.1687-2.24610.29121380.25612745X-RAY DIFFRACTION100
2.2461-2.33590.28841380.21982747X-RAY DIFFRACTION100
2.3359-2.4420.26451430.2082756X-RAY DIFFRACTION100
2.442-2.57050.26831520.19122776X-RAY DIFFRACTION100
2.5705-2.73120.24531420.19292795X-RAY DIFFRACTION100
2.7312-2.94140.25641620.18652736X-RAY DIFFRACTION100
2.9414-3.23630.24571400.1912822X-RAY DIFFRACTION100
3.2363-3.70190.24411520.17182815X-RAY DIFFRACTION100
3.7019-4.6540.18671620.14892831X-RAY DIFFRACTION100
4.654-19.80680.22571740.17262956X-RAY DIFFRACTION100

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