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- PDB-5jaq: Yersinia pestis FabV variant T276C -

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Basic information

Entry
Database: PDB / ID: 5jaq
TitleYersinia pestis FabV variant T276C
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / fatty acid biosynthesis FabV
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD binding / fatty acid biosynthetic process
Similarity search - Function
: / Trans-2-enoyl-CoA reductase / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic domain, putative / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic region / NAD(P)H binding domain of trans-2-enoyl-CoA reductase / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPschibul, A. / Kuper, J. / HIrschbeck, M. / Kisker, C.
CitationJournal: Biochemistry / Year: 2016
Title: Selectivity of Pyridone- and Diphenyl Ether-Based Inhibitors for the Yersinia pestis FabV Enoyl-ACP Reductase.
Authors: Neckles, C. / Pschibul, A. / Lai, C.T. / Hirschbeck, M. / Kuper, J. / Davoodi, S. / Zou, J. / Liu, N. / Pan, P. / Shah, S. / Daryaee, F. / Bommineni, G.R. / Lai, C. / Simmerling, C. / Kisker, C. / Tonge, P.J.
History
DepositionApr 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1065
Polymers44,2061
Non-polymers9004
Water5,477304
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-1 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.215, 102.215, 84.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 44205.875 Da / Num. of mol.: 1 / Mutation: T276C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: fabV, YPO4104, y4119, YP_4011 / Plasmid: pet15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8Z9U1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 150 mM (NH4)2SO4 100 mM MES pH 5.6-5.9 26.5-37.5 % PEG4000
PH range: 5.6-5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979934 Å / Relative weight: 1
ReflectionResolution: 1.9→44.26 Å / Num. obs: 39869 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.3
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bkr

4bkr


Resolution: 1.9→44.26 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.08
RfactorNum. reflection% reflection
Rfree0.2246 2003 5.03 %
Rwork0.1802 --
obs0.1824 39827 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 56 304 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083556
X-RAY DIFFRACTIONf_angle_d0.9344828
X-RAY DIFFRACTIONf_dihedral_angle_d13.1042143
X-RAY DIFFRACTIONf_chiral_restr0.051533
X-RAY DIFFRACTIONf_plane_restr0.005651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.27731440.28232622X-RAY DIFFRACTION97
1.9475-2.00020.32361340.25482661X-RAY DIFFRACTION98
2.0002-2.05910.25921400.23832655X-RAY DIFFRACTION98
2.0591-2.12550.26571390.21982671X-RAY DIFFRACTION98
2.1255-2.20150.25921450.21312662X-RAY DIFFRACTION98
2.2015-2.28960.28531500.21162686X-RAY DIFFRACTION98
2.2896-2.39380.24911450.20282674X-RAY DIFFRACTION98
2.3938-2.520.22941530.18052658X-RAY DIFFRACTION98
2.52-2.67790.2381470.19112704X-RAY DIFFRACTION99
2.6779-2.88460.23741410.1982732X-RAY DIFFRACTION99
2.8846-3.17480.24951570.18612707X-RAY DIFFRACTION99
3.1748-3.63410.24621300.16892765X-RAY DIFFRACTION99
3.6341-4.57780.16941560.13582761X-RAY DIFFRACTION99
4.5778-44.27240.16111220.15132866X-RAY DIFFRACTION98
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)
11.26850.02950.33793.42581.25133.1182-0.1118-0.0146-0.00960.21770.1377-0.1149-0.33460.2054-0.00080.2828-0.0228-0.00420.1125-0.02630.153842.5089-8.011716.408
20.72720.88680.79543.48071.35633.4675-0.1606-0.02030.0874-0.7189-0.27920.8862-0.5499-0.54290.0640.37030.0567-0.10040.1746-0.03870.357627.4917-11.95893.5915
30.6765-1.31220.02373.737-0.26211.60550.09860.0086-0.0983-0.53-0.02730.2983-0.2137-0.0056-0.09020.3304-0.0465-0.02290.1245-0.02980.189536.0451-12.7214-2.8381
41.131-0.42070.31953.85681.18072.8888-0.02720.164-0.1609-0.35640.1039-0.0975-0.04270.3054-0.00530.2352-0.07380.060.1397-0.0160.180243.3911-20.70264.8648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -5 through 114 )
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 238 )
3X-RAY DIFFRACTION3chain 'A' and (resid 239 through 315 )
4X-RAY DIFFRACTION4chain 'A' and (resid 316 through 399 )

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