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

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Basic information

Entry
Database: PDB / ID: 7fcm
TitleCrystal structure of Moraxella catarrhalis enoyl-ACP-reductase (FabI) in complex with NAD and Triclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / FabI / NADH / Triclosan
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 / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 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 the cofactor NAD
Authors: Katiki, M. / Neetu, N. / Pratap, S. / Kumar, P.
History
DepositionJul 15, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,6747
Polymers61,7282
Non-polymers1,9465
Water3,333185
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)127,34814
Polymers123,4564
Non-polymers3,89210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area23150 Å2
ΔGint-229 kcal/mol
Surface area33390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.520, 78.560, 89.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: -1 - 265 / Label seq-ID: 12 - 278

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 30864.008 Da / Num. of mol.: 2
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal, antibiotic, detergent*YM
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.14 Å3/Da / Density % sol: 42.62 % / 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, triclosan inhibitor

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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: Aug 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 26533 / % possible obs: 97.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.067 / Rrim(I) all: 0.138 / Χ2: 1.889 / Net I/σ(I): 8.3 / Num. measured all: 100946
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.21-2.252.10.5536850.6570.4160.6971.17451
2.25-2.293.30.47613340.6570.2980.5651.20599.3
2.29-2.333.50.62813240.7240.3790.7371.106100
2.33-2.383.70.52613490.7540.3110.6141.11299.9
2.38-2.433.80.52513480.8160.3050.611.109100
2.43-2.493.90.45513200.8460.260.5271.102100
2.49-2.553.90.42913560.8790.2420.4951.213100
2.55-2.6240.35513510.8970.1970.4091.219100
2.62-2.740.30313400.9250.1670.3471.375100
2.7-2.7840.27813650.9440.1530.3191.315100
2.78-2.8840.23513290.9570.1280.2691.411100
2.88-340.19813660.9620.1090.2271.541100
3-3.1440.1713580.9740.0930.1951.842100
3.14-3.340.1513610.9790.0830.1722.024100
3.3-3.5140.1213600.9840.0660.1382.4100
3.51-3.783.90.10213780.9890.0570.1182.83999.9
3.78-4.163.80.08713740.9890.0490.1013.35599.8
4.16-4.763.80.07213840.9950.0410.0833.4299.4
4.76-63.90.07614000.9920.0420.0883.43198.9
6-503.80.05414510.9970.0310.0632.58796.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FC8

7fc8


Resolution: 2.22→46.48 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.849 / SU ML: 0.165 / SU R Cruickshank DPI: 0.2919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1334 5 %RANDOM
Rwork0.1736 ---
obs0.1767 25158 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 212.91 Å2 / Biso mean: 40.445 Å2 / Biso min: 18.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.05 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.22→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 123 185 4321
Biso mean--33.38 45.62 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124205
X-RAY DIFFRACTIONr_angle_refined_deg1.531.625703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3635535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44322.553188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05615696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7221524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023138
Refine LS restraints NCS

Ens-ID: 1 / Number: 8296 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.221→2.279 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 80 -
Rwork0.265 1597 -
all-1677 -
obs--86.4 %

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