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- PDB-7f44: Crystal structure of Moraxella catarrhalis enoyl-ACP-reductase (F... -

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Basic information

Entry
Database: PDB / ID: 7f44
TitleCrystal structure of Moraxella catarrhalis enoyl-ACP-reductase (FabI) in complex with the cofactor NAD
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / FabI / NAD
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å
AuthorsKatiki, M. / Neetu, N. / Pratap, S. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BIC/12(29)/2013 India
Citation
Journal: Biochimie / Year: 2022
Title: Biochemical and structural basis for Moraxella catarrhalis enoyl-acyl carrier protein reductase (FabI) inhibition by triclosan and estradiol.
Authors: Katiki, M. / Neetu, N. / Pratap, S. / Kumar, P.
#1: Journal: To Be Published
Title: Crystal structure of Apo enoyl-ACP-reductase (FabI) from Moraxella catarrhalis
Authors: Katiki, M. / Pratap, S. / Kumar, P.
#2: Journal: To Be Published
Title: Crystal structure of enoyl-ACP-reductase (FabI) from Moraxella catarrhalis, in complex with NAD and Triclosan
Authors: Katiki, M. / Neetu, N. / Pratap, S. / Kumar, P.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 22, 2022ID: 6IWL
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 31, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)31,6604
Polymers30,8641
Non-polymers7963
Water1,00956
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)126,63816
Polymers123,4564
Non-polymers3,18212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area21490 Å2
ΔGint-193 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.500, 76.500, 99.725
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 30864.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (strain BBH18) (bacteria)
Strain: BBH18 / Gene: fabI, MCR_1078 / Plasmid: pET28C / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D5VCE0, 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.5 Å3/Da / Density % sol: 50.92 % / Description: Rod shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M calcium chloride, 0.1M HEPES buffer, 22% PEG 400, 10-folds of NADH cofactor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.12→60.7 Å / Num. obs: 17427 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.015 / Rrim(I) all: 0.051 / Net I/σ(I): 22.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.12-2.1911.22.8771867416630.4120.893.0150.899.7
8.21-47.558.70.022314336310.0080.02371.798.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CPG

7cpg
PDB Unreleased entry


Resolution: 2.12→47.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.786 / SU ML: 0.189 / SU R Cruickshank DPI: 0.2177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.253 857 5 %RANDOM
Rwork0.1963 ---
obs0.1992 16413 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.1 Å2 / Biso mean: 69.505 Å2 / Biso min: 39.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.93 Å2
Refinement stepCycle: final / Resolution: 2.12→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 51 56 2104
Biso mean--89.95 74.31 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122083
X-RAY DIFFRACTIONr_angle_refined_deg1.371.6192818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9965266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.93622.47393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59815348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8851512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021529
LS refinement shellResolution: 2.121→2.176 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 54 -
Rwork0.395 1093 -
all-1147 -
obs--91.1 %

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