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- PDB-7m1z: Targeting Enterococcus faecalis HMG-CoA reductase with a novel no... -

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Basic information

Entry
Database: PDB / ID: 7m1z
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 / homologyACETATE ION / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / (R)-MEVALONATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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: Nat Commun / 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 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 25, 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
C: Hydroxymethylglutaryl-CoA reductase, degradative
D: Hydroxymethylglutaryl-CoA reductase, degradative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,90233
Polymers187,4184
Non-polymers5,48429
Water6,125340
1
A: Hydroxymethylglutaryl-CoA reductase, degradative
B: Hydroxymethylglutaryl-CoA reductase, degradative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,09620
Polymers93,7092
Non-polymers3,38718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17620 Å2
ΔGint-92 kcal/mol
Surface area28110 Å2
MethodPISA
2
C: Hydroxymethylglutaryl-CoA reductase, degradative
D: Hydroxymethylglutaryl-CoA reductase, degradative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,80513
Polymers93,7092
Non-polymers2,09711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15400 Å2
ΔGint-108 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)241.289, 62.557, 171.925
Angle α, β, γ (deg.)90.000, 133.490, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Hydroxymethylglutaryl-CoA reductase, degradative


Mass: 46854.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The density for chain B extends into the plasmid construct. Chains D and A largely lack evidence for the C-terminal mobile flap region.
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: G5T22_00100 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A6M1FI83, hydroxymethylglutaryl-CoA reductase

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Non-polymers , 7 types, 369 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-HMG / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / (S)-HMG-COA


Mass: 906.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H39N7O20P3S
#7: Chemical ChemComp-MEV / (R)-MEVALONATE


Mass: 147.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5 mM NADP, 150 uM HMG-CoA, 0.1M MES pH 6.7, 50 mM colcium acetate, 8% PEG 8000. Protein at 10 mg/ml

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 76108 / % possible obs: 88.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 38.06 Å2 / Rmerge(I) obs: 0.088 / Χ2: 0.876 / Net I/σ(I): 9.7 / Num. measured all: 440737
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.26-2.344.10.44452490.605161.7
2.34-2.434.60.39758650.629169.3
2.43-2.555.20.33665510.643176.7
2.55-2.685.60.2772950.681185.6
2.68-2.855.90.21280970.743195.2
2.85-3.076.20.15785090.837199.8
3.07-3.386.30.11685410.9411100
3.38-3.866.30.0986111.1621100
3.86-4.876.30.07185871.345199.8
4.87-506.10.05188030.702199.9

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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: MOLECULAR REPLACEMENT
Starting model: 1R31

1r31


Resolution: 2.27→39.54 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 3840 5.05 %Random Selection
Rwork0.1958 72191 --
obs0.1979 76031 88.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.26 Å2 / Biso mean: 64.3973 Å2 / Biso min: 20.73 Å2
Refinement stepCycle: final / Resolution: 2.27→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11909 0 578 342 12829
Biso mean--65.93 48.64 -
Num. residues----1559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.27-2.30.3527880.27571410149847
2.3-2.330.28171050.27451822192761
2.33-2.360.283900.26091962205265
2.36-2.40.3271040.26072021212567
2.4-2.430.29131230.26172085220870
2.43-2.470.3481150.27352225234073
2.47-2.510.3071320.25072242237475
2.51-2.550.30811180.23852362248079
2.55-2.60.31521200.23272485260581
2.6-2.650.25781340.23032577271186
2.65-2.710.27451420.23912669281188
2.71-2.760.25651450.23512779292493
2.76-2.830.28291690.24132920308996
2.83-2.90.28511380.23912981311999
2.9-2.980.29291670.242230273194100
2.98-3.060.32481720.230729803152100
3.06-3.160.27771870.21630133200100
3.16-3.280.25181580.214130463204100
3.28-3.410.261680.207329903158100
3.41-3.560.23311640.198930603224100
3.56-3.750.21861580.18430223180100
3.75-3.990.21931630.175330573220100
3.99-4.290.19221630.153330463209100
4.29-4.720.17381440.144430653209100
4.72-5.410.20481490.159730923241100
5.41-6.810.25181740.195630923266100
6.81-39.540.19031500.17293161331198
Refinement TLS params.Method: refined / Origin x: 16.8338 Å / Origin y: -22.7408 Å / Origin z: 25.3202 Å
111213212223313233
T0.3529 Å20.0278 Å2-0.0159 Å2-0.4591 Å20.1127 Å2--0.2528 Å2
L1.6295 °2-0.0279 °2-0.1855 °2-0.203 °20.1235 °2--0.465 °2
S-0.0473 Å °-0.6562 Å °-0.18 Å °0.0821 Å °-0.0241 Å °0.0012 Å °0.0575 Å °-0.1046 Å °0.062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA13 - 370
2X-RAY DIFFRACTION1allB-4 - 501
3X-RAY DIFFRACTION1allC0 - 421
4X-RAY DIFFRACTION1allC501
5X-RAY DIFFRACTION1allD13 - 369
6X-RAY DIFFRACTION1allM1 - 4
7X-RAY DIFFRACTION1allG1 - 9
8X-RAY DIFFRACTION1allN1 - 8
9X-RAY DIFFRACTION1allR1 - 13
10X-RAY DIFFRACTION1allS1 - 402

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