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- PDB-4nqz: Crystal Structure of the Pseudomonas aeruginosa Enoyl-Acyl Carrie... -

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Basic information

Entry
Database: PDB / ID: 4nqz
TitleCrystal Structure of the Pseudomonas aeruginosa Enoyl-Acyl Carrier Protein Reductase (FabI) in apo form
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
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
D: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
E: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
F: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
G: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
H: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
I: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
J: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
K: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
L: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
M: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
N: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
O: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
P: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI


Theoretical massNumber of molelcules
Total (without water)465,71116
Polymers465,71116
Non-polymers00
Water6,431357
1
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


Theoretical massNumber of molelcules
Total (without water)116,4284
Polymers116,4284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-80 kcal/mol
Surface area32390 Å2
MethodPISA
2
E: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
F: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
G: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
H: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI


Theoretical massNumber of molelcules
Total (without water)116,4284
Polymers116,4284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-81 kcal/mol
Surface area32030 Å2
MethodPISA
3
I: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
J: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
K: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
L: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI


Theoretical massNumber of molelcules
Total (without water)116,4284
Polymers116,4284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-69 kcal/mol
Surface area32360 Å2
MethodPISA
4
M: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
N: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
O: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
P: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI


Theoretical massNumber of molelcules
Total (without water)116,4284
Polymers116,4284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-64 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.322, 155.844, 129.448
Angle α, β, γ (deg.)90.000, 111.060, 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.: 16
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 6% tacsimate, 8% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 132518 / Num. obs: 112296 / % possible obs: 84.74 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 37.74 Å2
Reflection shellResolution: 2.6→2.64 Å / % possible all: 67.7

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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: 2.604→44.394 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7723 / SU ML: 0.56 / σ(F): 1.48 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 5660 5.04 %random
Rwork0.1988 ---
obs0.2032 112296 84.74 %-
all-132518 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.83 Å2 / Biso mean: 40.21 Å2 / Biso min: 12.27 Å2
Refinement stepCycle: LAST / Resolution: 2.604→44.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29092 0 0 357 29449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929571
X-RAY DIFFRACTIONf_angle_d1.23739897
X-RAY DIFFRACTIONf_chiral_restr0.0454438
X-RAY DIFFRACTIONf_plane_restr0.0055264
X-RAY DIFFRACTIONf_dihedral_angle_d14.110560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6045-2.63410.37671230.31712645276863
2.6341-2.66510.36641410.31532913305469
2.6651-2.69760.42081310.29812956308770
2.6976-2.73170.39131550.30652922307770
2.7317-2.76760.41521570.31432936309371
2.7676-2.80550.38481630.30643026318972
2.8055-2.84560.41441650.29093080324573
2.8456-2.88810.35711740.26953111328575
2.8881-2.93320.41011800.26673256343678
2.9332-2.98130.33791810.25033297347879
2.9813-3.03270.34981780.25043394357281
3.0327-3.08780.32971850.25293472365782
3.0878-3.14720.33751910.24783472366384
3.1472-3.21140.33152070.24253588379586
3.2114-3.28120.35511910.2363637382887
3.2812-3.35750.31252130.223706391989
3.3575-3.44150.31751900.22053747393789
3.4415-3.53450.29452010.21783810401191
3.5345-3.63840.33092020.21723465366783
3.6384-3.75580.30511870.20013745393289
3.7558-3.890.27922060.18243970417694
3.89-4.04560.27542130.17763892410593
4.0456-4.22960.26892200.17033952417295
4.2296-4.45240.23722320.14734073430597
4.4524-4.73110.21822200.1424038425897
4.7311-5.09590.23172030.15694102430597
5.0959-5.60780.23912000.1524099429997
5.6078-6.41720.26442240.16664044426896
6.4172-8.0770.23872010.1484157435897
8.077-44.40090.19712260.15214131435796

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