[English] 日本語
Yorodumi
- PDB-4pv5: Crystal structure of mouse glyoxalase I in complexed with 18-beta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pv5
TitleCrystal structure of mouse glyoxalase I in complexed with 18-beta-glycyrrhetinic acid
ComponentsLactoylglutathione lyase
KeywordsLYASE/LYASE INHIBITOR / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


Pyruvate metabolism / lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding ...Pyruvate metabolism / lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Glyoxalase I signature 2. / Glyoxalase I / Glyoxalase I, conserved site / Glyoxalase I signature 1. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. ...Glyoxalase I signature 2. / Glyoxalase I / Glyoxalase I, conserved site / Glyoxalase I signature 1. / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-CBW / Lactoylglutathione lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, H. / Zhai, J. / Zhang, L.P. / Zhao, Y.N. / Li, C. / Hu, X.P.
CitationJournal: Acta Pharmacol.Sin. / Year: 2015
Title: Structural basis for 18-beta-glycyrrhetinic acid as a novel non-GSH analog glyoxalase I inhibitor
Authors: Zhang, H. / Huang, Q. / Zhai, J. / Zhao, Y.N. / Zhang, L.P. / Chen, Y.Y. / Zhang, R.W. / Li, Q. / Hu, X.P.
History
DepositionMar 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactoylglutathione lyase
B: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0105
Polymers41,4092
Non-polymers6023
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-127 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.825, 64.819, 63.483
Angle α, β, γ (deg.)90.00, 104.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Lactoylglutathione lyase / Glyoxalase I / Aldoketomutase / Glx I / Ketone-aldehyde mutase / Methylglyoxalase / S-D- ...Glyoxalase I / Aldoketomutase / Glx I / Ketone-aldehyde mutase / Methylglyoxalase / S-D-lactoylglutathione methylglyoxal lyase


Mass: 20704.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Glo1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(+) / References: UniProt: Q9CPU0, lactoylglutathione lyase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CBW / (3BETA,5BETA,14BETA)-3-HYDROXY-11-OXOOLEAN-12-EN-29-OIC ACID


Mass: 470.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H46O4 / Comment: antiinflammatory*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 30% PEG 2000, 50mM MES, 0.1M NaCl, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Sep 18, 2013
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25.86 Å / Num. obs: 16786 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.320.514199.6
6.96-24.780.024195.8

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZA0

2za0


Resolution: 2.3→22.258 Å / FOM work R set: 0.8248 / SU ML: 0.31 / σ(F): 1.36 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 744 5.06 %RANDOM
Rwork0.1766 13964 --
obs0.1801 14708 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.09 Å2 / Biso mean: 27.33 Å2 / Biso min: 7.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→22.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 36 109 2945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082920
X-RAY DIFFRACTIONf_angle_d1.2783973
X-RAY DIFFRACTIONf_chiral_restr0.085428
X-RAY DIFFRACTIONf_plane_restr0.006513
X-RAY DIFFRACTIONf_dihedral_angle_d14.2511095
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.47740.31731370.220827982935100
2.4774-2.72630.29241540.2227532907100
2.7263-3.11990.28161450.198127922937100
3.1199-3.92720.23851630.161827882951100
3.9272-22.25880.19731450.14992833297899

+
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://pdbjlvh1.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