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- PDB-6k23: NAD+ bound structure of enoyl-acyl carrier protein reductase (Fab... -

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Basic information

Entry
Database: PDB / ID: 6k23
TitleNAD+ bound structure of enoyl-acyl carrier protein reductase (FabI) from Acinetobacter baumanii
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / AbFabI / Rossman fold
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
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 / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSeol, G.B. / Park, H.J. / Ahn, Y.J. / Kang, L.W.
CitationJournal: To be published
Title: enoyl-acyl carrier protein reductase (FabI) from Acinetobacter baumanii
Authors: Kang, L.W.
History
DepositionMay 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8818
Polymers111,2274
Non-polymers2,6544
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19130 Å2
ΔGint-132 kcal/mol
Surface area34610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.183, 83.183, 174.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 27806.768 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: fabI_2, fabI, SAMEA104305177_04532, SAMEA104305337_07920
Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: V5VH25, UniProt: A0A336A0I9*PLUS, 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 7 / Details: 0.1 M HEPES pH 7.0 , 7% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 28104 / % possible obs: 96.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.032 / Rrim(I) all: 0.066 / Χ2: 2.234 / Net I/σ(I): 17.4 / Num. measured all: 104143
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.852.40.37313130.3070.2670.4620.96691
2.85-2.92.50.34913500.3810.2460.4311.04692.9
2.9-2.962.50.32413380.4450.2260.3981.0591.5
2.96-3.022.90.28513880.6330.1870.3431.13795
3.02-3.0830.27413610.6620.1750.3271.33594.4
3.08-3.153.10.24313970.7890.1530.2881.25195.4
3.15-3.233.30.20414130.8810.1240.241.41797.4
3.23-3.323.50.17214350.9280.1010.2011.41198.5
3.32-3.423.70.15814150.9510.0910.1831.79598
3.42-3.533.80.12914340.9730.0730.1481.82598.4
3.53-3.653.70.11614400.9740.0660.1341.91297.2
3.65-3.84.20.10314540.9840.0550.1172.75898.2
3.8-3.974.40.07914290.9910.0410.0892.44799.5
3.97-4.184.40.07214610.9920.0380.0822.82499.4
4.18-4.444.40.06214320.9940.0330.0713.18599.4
4.44-4.794.30.05814520.9940.0310.0663.40998.6
4.79-5.274.40.05414660.9950.0280.0613.27499.3
5.27-6.034.50.04814540.9950.0250.0542.82699
6.03-7.594.50.03814450.9980.0190.0422.32698.6
7.59-504.20.03412270.9960.0190.0392.33281.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NQZ

4nqz


Resolution: 2.8→40.49 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.286 / WRfactor Rwork: 0.2071 / FOM work R set: 0.768 / SU B: 22.142 / SU ML: 0.422 / SU Rfree: 0.4588 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2908 1388 4.9 %RANDOM
Rwork0.2192 ---
obs0.2228 26696 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 214.61 Å2 / Biso mean: 94.151 Å2 / Biso min: 56.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.8→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7820 0 176 8 8004
Biso mean--104.76 78.62 -
Num. residues----1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138156
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177608
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.63311064
X-RAY DIFFRACTIONr_angle_other_deg1.3291.57717580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06451036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22422.105380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77151308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6841548
X-RAY DIFFRACTIONr_chiral_restr0.0580.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021728
LS refinement shellResolution: 2.797→2.869 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 98 -
Rwork0.414 1888 -
all-1986 -
obs--91.61 %

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