[English] 日本語
Yorodumi
- PDB-8gdn: Structure of PmHMGR bound to mevalonate, CoA and NAD. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gdn
TitleStructure of PmHMGR bound to mevalonate, CoA and NAD.
Components3-hydroxy-3-methylglutaryl-coenzyme A reductase
KeywordsSTRUCTURAL PROTEIN / Non-Rossmann fold / Homodimer / Reductase / HMG-CoA
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-coenzyme A reductases signature 2. / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / 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.
Similarity search - Domain/homology
COENZYME A / (R)-MEVALONATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxy-3-methylglutaryl-coenzyme A reductase
Similarity search - Component
Biological speciesPseudomonas sp. 'mevalonii' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsPurohit, V. / Steussy, C.N. / Stauffacher, C.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM111645 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA023168 United States
CitationJournal: Biophys.J. / Year: 2024
Title: pH-dependent reaction triggering in PmHMGR crystals for time-resolved crystallography.
Authors: Purohit, V. / Steussy, C.N. / Rosales, A.R. / Critchelow, C.J. / Schmidt, T. / Helquist, P. / Wiest, O. / Mesecar, A. / Cohen, A.E. / Stauffacher, C.V.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxy-3-methylglutaryl-coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl-coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2008
Polymers91,2822
Non-polymers1,9176
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Electron density supports homodimerization of the enzyme monomer and binding of mentioned ligands.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14840 Å2
ΔGint-91 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.043, 226.043, 226.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 3-hydroxy-3-methylglutaryl-coenzyme A reductase


Mass: 45641.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. 'mevalonii' (bacteria) / Gene: mvaA / Plasmid: pKK-RED
Details (production host): Contained the mva operon in the expression vector pKK177-3
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P13702, hydroxymethylglutaryl-CoA reductase

-
Non-polymers , 5 types, 484 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MEV / (R)-MEVALONATE


Mass: 147.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.43 %
Description: Dimensions - 226.7110 226.7110 226.7110 90.0000 90.0000 90.0000 Symm - I 41 3 2
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 1.2 M ammonium sulfate, 100 mM ADA and 10 % glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 67257 / % possible obs: 100 % / Redundancy: 16.3 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.022 / Rrim(I) all: 0.094 / Χ2: 0.993 / Net I/σ(I): 8 / Num. measured all: 1095935
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.99-2.0613.12.97566310.30.6790.8463.0950.67899.9
2.06-2.1413.11.88166280.5390.8370.5381.9580.775100
2.14-2.2413.51.40266290.7760.9350.3951.4580.703100
2.24-2.3614.90.90466570.8710.9650.2420.9360.881100
2.36-2.5115.60.54566670.9510.9870.1420.5640.766100
2.51-2.716.30.36266810.9780.9940.0920.3740.899100
2.7-2.9718.90.267210.9930.9980.0470.2051.044100
2.97-3.419.20.12167430.9970.9990.0280.1251.235100
3.4-4.2919.60.07168020.99910.0160.0731.508100
4.29-5018.40.0417098110.010.0431.058100

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→48.19 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 2823 5.08 %
Rwork0.1808 --
obs0.183 55594 82.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5945 0 122 478 6545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086293
X-RAY DIFFRACTIONf_angle_d1.0738595
X-RAY DIFFRACTIONf_dihedral_angle_d10.377910
X-RAY DIFFRACTIONf_chiral_restr0.0581004
X-RAY DIFFRACTIONf_plane_restr0.0091118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.401330.281453X-RAY DIFFRACTION2
2.02-2.060.326100.3398211X-RAY DIFFRACTION7
2.06-2.10.2412260.2921636X-RAY DIFFRACTION20
2.1-2.140.27761090.26551944X-RAY DIFFRACTION62
2.14-2.190.27241520.24852892X-RAY DIFFRACTION92
2.19-2.240.30941650.26613000X-RAY DIFFRACTION96
2.24-2.30.35991630.30513034X-RAY DIFFRACTION96
2.3-2.360.24431560.21643145X-RAY DIFFRACTION99
2.36-2.430.27141540.19743129X-RAY DIFFRACTION99
2.43-2.510.25722140.20093054X-RAY DIFFRACTION99
2.51-2.60.25891650.20383117X-RAY DIFFRACTION99
2.6-2.70.22841890.20823088X-RAY DIFFRACTION98
2.7-2.820.24461460.19763121X-RAY DIFFRACTION98
2.82-2.970.2271710.19263108X-RAY DIFFRACTION97
2.97-3.160.26541870.18793087X-RAY DIFFRACTION97
3.16-3.40.20591560.1723113X-RAY DIFFRACTION98
3.4-3.740.18221480.15073177X-RAY DIFFRACTION98
3.75-4.290.19551520.13273198X-RAY DIFFRACTION98
4.29-5.40.16521770.13723234X-RAY DIFFRACTION99
5.4-48.190.20411800.16573430X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 88.4342 Å / Origin y: 129.1362 Å / Origin z: 118.6944 Å
111213212223313233
T0.1405 Å20.0691 Å20.0345 Å2-0.1645 Å2-0.0466 Å2--0.2393 Å2
L0.6831 °20.0643 °2-0.0898 °2-0.778 °20.2119 °2--0.7853 °2
S-0.0095 Å °-0.0016 Å °0.1716 Å °0.0089 Å °-0.0602 Å °0.1547 Å °-0.0921 Å °-0.0854 Å °0.042 Å °
Refinement TLS groupSelection details: all

+
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