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- PDB-7fc8: Crystal structure of the Apo enoyl-ACP-reductase (FabI) from Mora... -

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Basic information

Entry
Database: PDB / ID: 7fc8
TitleCrystal structure of the Apo enoyl-ACP-reductase (FabI) from Moraxella catarrhalis
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / FabI / NAD
Function / homologyenoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / Enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / fatty acid biosynthetic process / NAD(P)-binding domain superfamily / Enoyl-[acyl-carrier-protein] reductase [NADH]
Function and homology information
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.377 Å
AuthorsKatiki, M. / 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 Moraxella catarrhalis enoyl-ACP-reductase (FabI) in complex with the cofactor NAD
Authors: Katiki, M. / Neetu, N. / 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
DepositionJul 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 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 / citation_author
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)30,9042
Polymers30,8641
Non-polymers401
Water90150
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)123,6168
Polymers123,4564
Non-polymers1604
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 area11320 Å2
ΔGint-135 kcal/mol
Surface area36980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.982, 74.982, 101.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-301-

CA

21A-449-

HOH

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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)
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.76 % / 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 12183 / % possible obs: 97.5 % / Redundancy: 10.1 % / Biso Wilson estimate: 50.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Χ2: 1.532 / Net I/σ(I): 46.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Χ2% possible all
2.36-2.45.40.5283090.9041.57851.4
2.4-2.449.20.476121.339100
2.44-2.499.90.5536051.131100
2.49-2.5410.20.5446061.026100
2.54-2.610.20.56061.03100
2.6-2.6610.30.3496211.032100
2.66-2.7210.40.3255961.046100
2.72-2.810.30.2826281.097100
2.8-2.8810.40.2316121.169100
2.88-2.9710.50.1836081.28100
2.97-3.0810.40.1546101.367100
3.08-3.210.50.1276181.403100
3.2-3.3510.60.16231.637100
3.35-3.5310.50.0786221.86199.8
3.53-3.7510.50.0676302.092100
3.75-4.0310.50.0556242.273100
4.03-4.4410.30.0486462.33799.8
4.44-5.0810.40.0416402.215100
5.08-6.410.20.0386571.776100
6.4-509.50.0297101.76897.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZJU

4zju


Resolution: 2.377→31.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.821 / SU ML: 0.198 / SU R Cruickshank DPI: 0.3288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 596 4.9 %RANDOM
Rwork0.1999 ---
obs0.2029 11554 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167.64 Å2 / Biso mean: 61.733 Å2 / Biso min: 27.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å2-0 Å2
2--1.11 Å20 Å2
3----2.21 Å2
Refinement stepCycle: final / Resolution: 2.377→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 1 50 1873
Biso mean--129.93 54.78 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121846
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6132490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8215240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7112285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.50915322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4041512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021350
LS refinement shellResolution: 2.377→2.438 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.347 43 -
Rwork0.327 784 -
obs--93.87 %

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