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- PDB-7m66: Targeting Enterococcus faecalis HMG-CoA reductase with a novel no... -

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Basic information

Entry
Database: PDB / ID: 7m66
TitleTargeting Enterococcus faecalis HMG-CoA reductase with a novel non-statin inhibitor
ComponentsHydroxymethylglutaryl-CoA reductase, degradative
KeywordsANTIMICROBIAL PROTEIN / antibiotic / bacterial / HMG-CoA reductase
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase (NADPH) activity / acetyl-CoA C-acetyltransferase / coenzyme A metabolic process / acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding
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, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å
AuthorsBose, S. / Steussy, C.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL52115 United States
CitationJournal: Commun Biol / Year: 2023
Title: Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor.
Authors: Bose, S. / Steussy, C.N. / Lopez-Perez, D. / Schmidt, T. / Kulathunga, S.C. / Seleem, M.N. / Lipton, M. / Mesecar, A.D. / Rodwell, V.W. / Stauffacher, C.V.
History
DepositionMar 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)186,87631
Polymers184,4224
Non-polymers2,45427
Water11,638646
1
A: Hydroxymethylglutaryl-CoA reductase, degradative
B: Hydroxymethylglutaryl-CoA reductase, degradative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,59817
Polymers92,2112
Non-polymers1,38715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12510 Å2
ΔGint-86 kcal/mol
Surface area26380 Å2
MethodPISA
2
C: Hydroxymethylglutaryl-CoA reductase, degradative
D: Hydroxymethylglutaryl-CoA reductase, degradative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,27814
Polymers92,2112
Non-polymers1,06712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-102 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.661, 168.661, 120.194
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Hydroxymethylglutaryl-CoA reductase, degradative


Mass: 46105.559 Da / Num. of mol.: 4
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

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Non-polymers , 6 types, 673 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: MES, calcium acetate, PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 91453 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 38.65 Å2 / Rmerge(I) obs: 0.116 / Χ2: 1.123 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.25-2.330.66590840.952199.8
2.33-2.420.44590750.953199.9
2.42-2.530.32291380.921199.9
2.53-2.670.24591240.9631100
2.67-2.830.1991240.9971100
2.83-3.050.14591201.0181100
3.05-3.360.11291491.131100
3.36-3.850.10191781.4421100
3.85-4.850.09691851.4021100
4.85-500.09492761.331199.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.25→45.13 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 4591 5.02 %
Rwork0.1749 86813 -
obs0.1766 91404 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.11 Å2 / Biso mean: 51.1281 Å2 / Biso min: 23.32 Å2
Refinement stepCycle: final / Resolution: 2.25→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10935 0 287 648 11870
Biso mean--63.56 43.44 -
Num. residues----1437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.280.45261290.38762746287594
2.28-2.310.3251690.270328653034100
2.31-2.330.31161500.255228663016100
2.33-2.360.2781520.231428723024100
2.36-2.390.26861840.212428893073100
2.39-2.430.23931530.220628693022100
2.43-2.460.29051530.208828943047100
2.46-2.50.23151510.20329023053100
2.5-2.540.2641470.200328843031100
2.54-2.580.21891460.197728853031100
2.58-2.620.23251500.200329213071100
2.62-2.670.24661580.202228893047100
2.67-2.720.25541390.20529373076100
2.72-2.780.25151530.210728493002100
2.78-2.840.24661520.213829073059100
2.84-2.90.29881530.211628973050100
2.9-2.980.20481600.203828843044100
2.98-3.060.23851390.193829163055100
3.06-3.150.21051830.18728713054100
3.15-3.250.22651640.188829013065100
3.25-3.360.20381360.183829033039100
3.36-3.50.20831490.183229203069100
3.5-3.660.18861560.164628903046100
3.66-3.850.16821490.154229273076100
3.85-4.090.17221360.140529093045100
4.09-4.410.15891420.133329333075100
4.41-4.850.1741530.126329173070100
4.85-5.550.16851580.141929133071100
5.55-6.990.19981660.166429293095100
6.99-45.130.17921610.1552928308998

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