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- PDB-4cv3: Crystal structure of E. coli FabI in complex with NADH and PT166 -

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Basic information

Entry
Database: PDB / ID: 4cv3
TitleCrystal structure of E. coli FabI in complex with NADH and PT166
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE SUPERFAMILY / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / ECFABI
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / biotin biosynthetic process / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-VT4 / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsEltschkner, S. / Schiebel, J. / Chang, A. / Shah, S. / Tonge, P.J. / Kisker, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (Acp) Reductase Inhibitor.
Authors: Schiebel, J. / Chang, A. / Shah, S. / Lu, Y. / Liu, L. / Pan, P. / Hirschbeck, M.W. / Tareilus, M. / Eltschkner, S. / Yu, W. / Cummings, J.E. / Knudson, S.E. / Bommineni, G.R. / Walker, S.G. ...Authors: Schiebel, J. / Chang, A. / Shah, S. / Lu, Y. / Liu, L. / Pan, P. / Hirschbeck, M.W. / Tareilus, M. / Eltschkner, S. / Yu, W. / Cummings, J.E. / Knudson, S.E. / Bommineni, G.R. / Walker, S.G. / Slayden, R.A. / Sotriffer, C.A. / Tonge, P.J. / Kisker, C.
History
DepositionMar 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)59,8586
Polymers57,9282
Non-polymers1,9304
Water4,432246
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)119,71612
Polymers115,8564
Non-polymers3,8598
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area21360 Å2
ΔGint-113.5 kcal/mol
Surface area28760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.678, 79.678, 330.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-2098-

HOH

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Components

#1: Protein ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] / ENOYL-ACP REDUCTASE


Mass: 28964.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C6EFU4, UniProt: A0A140NA83*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-VT4 / 2-hexyl-1-methyl-5-(2-methylphenoxy)pyridin-4(1H)-one


Mass: 299.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25NO2
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.69 Å3/Da / Density % sol: 54.3 % / Description: NONE
Crystal growpH: 5.6 / Details: 0.1 M NA-CITRATE PH 5.6, 0.2 M NH4AC, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0644
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0644 Å / Relative weight: 1
ReflectionResolution: 1.95→47.7 Å / Num. obs: 46243 / % possible obs: 99.5 % / Observed criterion σ(I): 6 / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.7 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QSG

1qsg


Resolution: 1.95→69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.621 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO VERY WEAK ELECTRON DENSITY, THE LOOP REGION 193-209 WAS NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.21206 2338 5.1 %RANDOM
Rwork0.1762 ---
obs0.17799 43820 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.903 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.95→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 132 246 3914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223768
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9625115
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2755484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38224.172151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14615587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6161521
X-RAY DIFFRACTIONr_chiral_restr0.1090.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213067
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_it1.7321.52379
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.58623781
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.16131389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1454.51329
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 173 -
Rwork0.225 3092 -
obs--97.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4277-0.04670.19380.11540.14740.3690.005-0.02890.0126-0.00450.0575-0.0214-0.00620.1115-0.06250.01650.01450.00040.1583-0.05110.0826-20.581230.2118-13.9927
20.40850.2369-0.14650.24640.15620.62580.0056-0.05420.0501-0.0236-0.01130.0447-0.020.05510.00570.05050.0335-0.00750.1283-0.02370.0798-33.507429.7573-20.8187
37.40630.91441.53361.39350.59312.3473-0.025-0.551-0.21620.2645-0.08480.09680.2881-0.06740.10970.12130.02450.02860.09070.01370.0294-36.138810.2008-13.1766
40.19530.33490.32060.60920.61630.65730.0323-0.01070.04430.05330.00590.01810.06660.0398-0.03820.04550.0523-0.00580.1232-0.04050.1099-31.591518.1272-23.8174
50.5152-0.37690.00070.55630.34890.4482-0.0386-0.06290.0367-0.1538-0.04760.0192-0.2293-0.11170.08620.12580.0794-0.05060.0926-0.05070.1074-51.475650.6117-17.4572
60.59710.046-0.08650.05740.07930.2458-0.0216-0.06450.0108-0.0585-0.06840.0256-0.1014-0.03970.090.06990.047-0.01430.1169-0.03590.0992-46.00937.6233-21.6431
72.2552-0.9557-1.92285.45094.67994.63330.14240.28780.015-0.6471-0.0696-0.1829-0.6218-0.2366-0.07280.18330.0603-0.08220.0608-0.03980.1357-52.35941.8944-41.1495
80.38670.25860.31550.71070.5530.4771-0.0353-0.07850.0019-0.1691-0.04970.0934-0.1233-0.07030.0850.08460.0727-0.03460.1095-0.04510.1143-55.251836.0472-29.2533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 147
2X-RAY DIFFRACTION2A148 - 192
3X-RAY DIFFRACTION3A210 - 223
4X-RAY DIFFRACTION4A224 - 257
5X-RAY DIFFRACTION5B2 - 147
6X-RAY DIFFRACTION6B148 - 192
7X-RAY DIFFRACTION7B210 - 223
8X-RAY DIFFRACTION8B224 - 257

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