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- PDB-7m3h: Targeting Enterococcus faecalis HMG-CoA reductase with a novel no... -

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Basic information

Entry
Database: PDB / ID: 7m3h
TitleTargeting Enterococcus faecalis HMG-CoA reductase with a novel non-statin inhibitor
ComponentsHydroxymethylglutaryl-CoA reductase, degradative
KeywordsANTIBIOTIC / ligands / metabolism / drug target / hmg-coa / mevalonate / prokaryote.
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-coenzyme A reductases signature 3. / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, conserved site / Hydroxymethylglutaryl-coenzyme A reductase / Hydroxymethylglutaryl-coenzyme A reductases family profile. / Thiolase, active site ...Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-coenzyme A reductases signature 3. / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, conserved site / Hydroxymethylglutaryl-coenzyme A reductase / Hydroxymethylglutaryl-coenzyme A reductases family profile. / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
Chem-YPV / Hydroxymethylglutaryl-CoA reductase, degradative
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsBose, S. / Steussy, C.N. / Stauffacher, C.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL52115 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)MH082373 United States
CitationJournal: To Be Published
Title: Targeting Enterococcus faecalis HMG-CoA reductase with a novel non-statin inhibitor
Authors: Bose, S. / Steussy, C.N. / Stauffacher, C.V.
History
DepositionMar 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxymethylglutaryl-CoA reductase, degradative
B: Hydroxymethylglutaryl-CoA reductase, degradative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2388
Polymers92,2112
Non-polymers1,0276
Water17,529973
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-124 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.503, 81.126, 152.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hydroxymethylglutaryl-CoA reductase, degradative


Mass: 46105.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EY666_03235 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4U3MLJ4, hydroxymethylglutaryl-CoA reductase
#2: Chemical ChemComp-YPV / 5-[(4-butylphenyl)sulfamoyl]-2-hydroxybenzoic acid


Mass: 349.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19NO5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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.: 973 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 25% PEG 4000, 0.17 M sodium acetate, 0.085 M Tris-HCl at pH 8.5, 2% glycerol

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95372 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.27→50 Å / Num. obs: 237239 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 13.06 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.09 / Net I/σ(I): 10.2 / Num. measured all: 1238458
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.27-1.325.10.966234081.106199.7
1.32-1.375.10.721235281.1311100
1.37-1.435.20.533235911.1281100
1.43-1.515.20.35235711.1281100
1.51-1.65.20.244235861.1821100
1.6-1.725.20.168236821.0681100
1.72-1.95.30.098236891.0671100
1.9-2.175.30.075238001.041100
2.17-2.745.30.05239361.0451100
2.74-505.30.032244481.013199.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MIZ

7miz


Resolution: 1.27→44.15 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1656 2386 1.01 %
Rwork0.1523 234731 -
obs0.1524 237117 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.34 Å2 / Biso mean: 20.0112 Å2 / Biso min: 6.32 Å2
Refinement stepCycle: final / Resolution: 1.27→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 0 105 985 7323
Biso mean--17.34 31.17 -
Num. residues----819
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.27-1.30.27291470.2785133951354298
1.3-1.320.25061410.25441367813819100
1.32-1.350.23581340.23471370513839100
1.35-1.390.21851260.22411372813854100
1.39-1.430.2371530.20721373513888100
1.43-1.470.20381370.19271374013877100
1.47-1.510.18961460.17821375213898100
1.51-1.570.17671230.16911375913882100
1.57-1.630.1871490.16191377213921100
1.63-1.710.1661530.15261375713910100
1.71-1.80.20731350.14851380313938100
1.8-1.910.14311310.14341385913990100
1.91-2.060.17021290.13991385013979100
2.06-2.260.15081390.13311390014039100
2.26-2.590.14881400.13141395014090100
2.59-3.260.15021370.13591403514172100
3.26-44.150.14441660.1414143131447999

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