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- PDB-6ah9: Crystal structure of enoyl-ACP reductase from Acinetobacter bauma... -

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Basic information

Entry
Database: PDB / ID: 6ah9
TitleCrystal structure of enoyl-ACP reductase from Acinetobacter baumannii in complex with NAD and Triclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Fabi / Acinetobacter baumannii / NAD / Triclosan / Inhibitor complex
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 speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRani, S.T. / Nataraj, V. / Laxminarasimhan, A. / Thomas, A. / Krishnamurthy, N.
CitationJournal: To Be Published
Title: Crystal structure of enoyl-ACP reductase from Acinetobacter baumannii in complex with NAD and Triclosan
Authors: Rani, S.T. / Nataraj, V. / Laxminarasimhan, A. / Thomas, A. / Krishnamurthy, N.
History
DepositionAug 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,6143
Polymers28,6611
Non-polymers9532
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-30 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.212, 77.245, 85.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

21A-520-

HOH

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Components

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


Mass: 28660.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Strain: ATCC 19606 / AUCC 669 / Gene: NC_009085.1 / Plasmid: pET 28a-AbFabI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2J1CZK4, UniProt: D0CAD5*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 0.1M MES pH 5.5, 100mM NaCl, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2018
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→72.6 Å / Num. obs: 26533 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.3
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4 / Num. unique obs: 1390 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZJU

4zju


Resolution: 1.74→57.23 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.932 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24081 1316 5 %RANDOM
Rwork0.19544 ---
obs0.19776 25180 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.352 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.74→57.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 61 144 2146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192043
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.9932775
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2725259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.05623.7882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46915316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0831512
X-RAY DIFFRACTIONr_chiral_restr0.1360.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211538
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1462.2611039
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0463.3741297
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2442.5791000
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined16.39334.9783331
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.737→1.782 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 70 -
Rwork0.25 1827 -
obs--96.69 %

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