[English] 日本語
Yorodumi
- PDB-7m1z: Targeting Enterococcus faecalis HMG-CoA reductase with a novel no... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7m1z
TitleTargeting Enterococcus faecalis HMG-CoA reductase with a novel non-statin inhibitor
Componentsacetyl-CoA C-acetyltransferase
KeywordsANTIBIOTIC / ligands / metabolism / drug target / hmg-coa / mevalonate / prokaryote.
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
Helicase, Ruva Protein; domain 3 - #660 / Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / 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 ...Helicase, Ruva Protein; domain 3 - #660 / Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / 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 / Helicase, Ruva Protein; domain 3 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / (R)-MEVALONATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / acetyl-CoA C-acetyltransferase
Similarity search - Component
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
Revision 1.3Mar 26, 2025Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entry_details.has_protein_modification / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: acetyl-CoA C-acetyltransferase
B: acetyl-CoA C-acetyltransferase
C: acetyl-CoA C-acetyltransferase
D: acetyl-CoA C-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,90233
Polymers187,4184
Non-polymers5,48429
Water6,125340
1
A: acetyl-CoA C-acetyltransferase
B: acetyl-CoA C-acetyltransferase
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: acetyl-CoA C-acetyltransferase
D: acetyl-CoA C-acetyltransferase
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

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
acetyl-CoA C-acetyltransferase / Acetoacetyl-CoA thiolase


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: EY666_03235 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4U3MLJ4, acetyl-CoA C-acetyltransferase

-
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

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more