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- PDB-4nr0: Crystal structure of the Pseudomonas aeruginosa Enoyl-Acyl Carrie... -

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Basic information

Entry
Database: PDB / ID: 4nr0
TitleCrystal structure of the Pseudomonas aeruginosa Enoyl-Acyl Carrier Protein Reductase (FabI) in complex with NAD+ and triclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH] FabI
KeywordsOXIDOREDUCTASE / Rossmann fold motif / reductase / cytosol
Function / homology
Function and homology information


fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / identical protein 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] FabI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsChi, Y.M. / Lee, J.H. / Park, A.K.
CitationJournal: Bull.Korean Chem.Soc. / Year: 2015
Title: Crystal Structures of Pseudomonas aeruginosa Enoyl-ACP Reductase (FabI) in the Presence and Absence of NAD+ and Triclosan
Authors: Lee, J.H. / Park, A.K. / Chi, Y.M. / Jeong, S.W.
History
DepositionNov 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Nov 8, 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 [NADH] FabI
B: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
C: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
D: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,24012
Polymers116,4284
Non-polymers3,8128
Water14,538807
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21750 Å2
ΔGint-205 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.784, 107.573, 73.517
Angle α, β, γ (deg.)90.000, 116.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29106.936 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fabI, PA1806 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9ZFE4, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 1.97 Å3/Da / Density % sol: 37.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M sodium malonate pH 5.0, 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.12713 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. all: 83699 / Num. obs: 74501 / % possible obs: 89.01 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.799→1.83 Å / % possible all: 52.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1c14

1c14


Resolution: 1.799→41.691 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.889 / SU ML: 0.16 / σ(F): 1.53 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1783 3735 5.01 %random
Rwork0.1456 ---
all0.1473 83699 --
obs0.1473 74501 89.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.15 Å2 / Biso mean: 16.9908 Å2 / Biso min: 5.95 Å2
Refinement stepCycle: LAST / Resolution: 1.799→41.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7698 0 244 807 8749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078088
X-RAY DIFFRACTIONf_angle_d1.16710942
X-RAY DIFFRACTIONf_chiral_restr0.0511206
X-RAY DIFFRACTIONf_plane_restr0.0051406
X-RAY DIFFRACTIONf_dihedral_angle_d13.1892830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7994-1.82220.2124560.18811187124341
1.8222-1.84610.2542800.17431405148547
1.8461-1.87140.2412770.16671603168055
1.8714-1.89820.1977970.161806190361
1.8982-1.92650.2009890.15041989207867
1.9265-1.95660.18821090.14912159226874
1.9566-1.98870.21311210.14322380250180
1.9887-2.0230.19551560.14632559271589
2.023-2.05970.20911570.14922740289793
2.0597-2.09940.17141580.14862933309199
2.0994-2.14220.15681520.143628713023100
2.1422-2.18880.17551450.144529253070100
2.1888-2.23970.18771500.145729523102100
2.2397-2.29570.21831470.150229443091100
2.2957-2.35780.21081500.146529153065100
2.3578-2.42710.18571490.145629363085100
2.4271-2.50550.19931630.152729533116100
2.5055-2.5950.20081560.146328993055100
2.595-2.69890.21811460.150529753121100
2.6989-2.82170.18521460.157129623108100
2.8217-2.97040.18341720.153929103082100
2.9704-3.15650.18591520.157129353087100
3.1565-3.40010.15611530.147329683121100
3.4001-3.74210.19121740.150429313105100
3.7421-4.28310.13661510.127929753126100
4.2831-5.39440.14891670.125729703137100
5.3944-41.70190.141620.1352984314699

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