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- PDB-4cv2: Crystal structure of E. coli FabI in complex with NADH and CG400549 -

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Basic information

Entry
Database: PDB / ID: 4cv2
TitleCrystal structure of E. coli FabI in complex with NADH and CG400549
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 activity (NAD(P)H) / 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-PT6 / 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: 1.8 Å
AuthorsTareilus, M. / 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)59,9406
Polymers57,9282
Non-polymers2,0124
Water6,395355
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)119,88012
Polymers115,8564
Non-polymers4,0248
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area18620 Å2
ΔGint-104.5 kcal/mol
Surface area28910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.108, 80.108, 320.186
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
11A-2202-

HOH

21B-2137-

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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-PT6 / 1-(3-amino-2-methylbenzyl)-4-[2-(thiophen-2-yl)ethoxy]pyridin-2(1H)-one


Mass: 340.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N2O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 10.5 / Details: 0.2 M NH4AC, 0.1 M CAPS PH 10.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→47.1 Å / Num. obs: 56987 / % possible obs: 98.7 % / Observed criterion σ(I): 6 / Redundancy: 14.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.3 / % possible all: 96.6

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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: 1.8→69.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.391 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO VERY WEAK ELECTRON DENSITY, THE LOOP REGION 193-210 WAS NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.20704 2892 5.1 %RANDOM
Rwork0.17472 ---
obs0.17639 53952 98.57 %-
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: 33.009 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→69.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 136 355 4006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9635137
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78924.183153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84515593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8951521
X-RAY DIFFRACTIONr_chiral_restr0.0950.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213126
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_it1.351.52369
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97523768
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.31831412
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8684.51361
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 222 -
Rwork0.244 3785 -
obs--96.37 %
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)
10.7039-0.05220.36270.20980.0080.26930.0176-0.01020.02760.01820.0372-0.06310.0090.1044-0.05490.0170.0085-0.00820.1539-0.09410.0656-18.428330.0034-13.8542
20.6244-0.077-0.06980.57630.18050.34890.0005-0.00470.0375-0.01560.02170.00450.02220.0485-0.02220.02060.0351-0.02230.1065-0.05770.035-31.904729.2701-20.7184
314.77936.13011.45644.66621.16251.35960.1418-1.0653-0.1650.1874-0.28850.05560.1968-0.08170.14660.1020.0437-0.02630.1508-0.01520.0599-33.283210.0548-12.4414
40.7029-0.4994-0.13710.68530.35530.9020.04920.048-0.06880.04690.00030.00470.04950.0237-0.04950.04280.0504-0.03920.1154-0.07060.0489-30.047717.3804-22.9308
51.5265-0.09480.3611.24590.45141.4766-0.0746-0.05780.2913-0.1281-0.14860.112-0.2902-0.20170.22320.09650.0942-0.08780.1044-0.09360.1227-55.789654.1638-17.0373
60.8435-0.2373-0.07190.43320.29790.30730.002-0.00260.113-0.0778-0.04180.007-0.0922-0.04390.03980.04180.033-0.02510.0764-0.04960.0495-42.122241.5832-19.4867
71.7259-0.15040.07051.25921.21611.3616-0.00030.09140.1425-0.2381-0.0510.0128-0.1906-0.05340.05130.08670.047-0.04040.0689-0.0540.0715-53.169836.7853-32.1356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 147
2X-RAY DIFFRACTION2A148 - 192
3X-RAY DIFFRACTION3A212 - 223
4X-RAY DIFFRACTION4A224 - 257
5X-RAY DIFFRACTION5B2 - 87
6X-RAY DIFFRACTION6B88 - 192
7X-RAY DIFFRACTION7B211 - 257

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