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- PDB-5jam: Yersinia pestis FabV variant T276V -

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Basic information

Entry
Database: PDB / ID: 5jam
TitleYersinia pestis FabV variant T276V
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 / fatty acid biosynthetic process / NAD binding
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: 2 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)45,1025
Polymers44,2021
Non-polymers9004
Water1,838102
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-1 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.872, 102.872, 84.794
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: 44201.863 Da / Num. of mol.: 1 / Mutation: T276V
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 / Nicotinamide adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 102 / 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 25-38% PEG 4000 100 mM MES PH 5.6-5.9
PH range: 5.6-5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→44.55 Å / Num. obs: 35422 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10 % / CC1/2: 0.997 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.885 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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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: 2→44.545 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.96
RfactorNum. reflection% reflection
Rfree0.2273 1772 5.01 %
Rwork0.201 --
obs0.2023 35384 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→44.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 56 102 3254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023535
X-RAY DIFFRACTIONf_angle_d0.594802
X-RAY DIFFRACTIONf_dihedral_angle_d11.4442127
X-RAY DIFFRACTIONf_chiral_restr0.042534
X-RAY DIFFRACTIONf_plane_restr0.003646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05410.36041170.3232582X-RAY DIFFRACTION100
2.0541-2.11460.33941480.29712539X-RAY DIFFRACTION100
2.1146-2.18280.29941380.28512560X-RAY DIFFRACTION100
2.1828-2.26090.3111380.25872543X-RAY DIFFRACTION100
2.2609-2.35140.24331460.24262539X-RAY DIFFRACTION100
2.3514-2.45840.27061270.23042577X-RAY DIFFRACTION100
2.4584-2.5880.27261530.22832565X-RAY DIFFRACTION100
2.588-2.75010.23931310.21172560X-RAY DIFFRACTION100
2.7501-2.96240.23851380.21992592X-RAY DIFFRACTION100
2.9624-3.26040.24211450.20192575X-RAY DIFFRACTION100
3.2604-3.7320.17791290.1872610X-RAY DIFFRACTION100
3.732-4.70110.17011430.14772623X-RAY DIFFRACTION100
4.7011-44.55590.20391190.16862747X-RAY DIFFRACTION100
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)
13.17091.59981.17292.22330.1473.02480.0050.05410.0010.0731-0.0526-0.0531-0.19820.50630.0470.1722-0.0686-0.00190.3397-0.00480.136415.541-38.03970.9131
22.96341.15911.63830.67120.29962.7869-0.49340.24340.6297-0.1575-0.04510.3068-0.6559-0.06870.20120.3493-0.0495-0.09790.36290.07260.4070.5444-29.2325-10.3023
31.40622.61980.17062.6795-0.26421.183-0.28660.40350.138-0.2560.32150.4227-0.07070.2919-0.0690.2631-0.1163-0.04760.49920.02080.19555.5817-38.1551-17.1393
42.79181.44271.29052.06770.63413.134-0.03960.3917-0.1946-0.14970.10440.01780.24180.2836-0.01110.21210.00220.010.3547-0.04290.16353.9073-48.1928-9.1673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -5 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 218 )
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 315 )
4X-RAY DIFFRACTION4chain 'A' and (resid 316 through 399 )

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