[English] 日本語
Yorodumi
- PDB-1qh3: HUMAN GLYOXALASE II WITH CACODYLATE AND ACETATE IONS PRESENT IN T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qh3
TitleHUMAN GLYOXALASE II WITH CACODYLATE AND ACETATE IONS PRESENT IN THE ACTIVE SITE
ComponentsPROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE)
KeywordsHYDROLASE / METALLO-HYDROLASE
Function / homology
Function and homology information


hydroxyacylglutathione hydrolase / hydroxyacylglutathione hydrolase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / glutathione biosynthetic process / Pyruvate metabolism / glutathione metabolic process / mitochondrial matrix / mitochondrion / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Hydroxyacylglutathione hydrolase / Hydroxyacylglutathione hydrolase, C-terminal domain / Hydroxyacylglutathione hydrolase, MBL domain / Hydroxyacylglutathione hydrolase C-terminus / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Hydroxyacylglutathione hydrolase / Hydroxyacylglutathione hydrolase, C-terminal domain / Hydroxyacylglutathione hydrolase, MBL domain / Hydroxyacylglutathione hydrolase C-terminus / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / : / Hydroxyacylglutathione hydrolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsCameron, A.D. / Ridderstrom, M. / Olin, B. / Mannervik, B.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of human glyoxalase II and its complex with a glutathione thiolester substrate analogue.
Authors: Cameron, A.D. / Ridderstrom, M. / Olin, B. / Mannervik, B.
History
DepositionMay 10, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Sep 24, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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: PROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE)
B: PROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,88115
Polymers57,8082
Non-polymers1,07313
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.080, 72.370, 162.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99956, -0.01683, 0.02444), (0.02932, -0.68737, 0.72572), (0.00459, 0.72612, 0.68756)
Vector: 26.02553, 46.35559, -17.67834)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein PROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE) / GLYOXALASE II


Mass: 28904.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: LIVER / Description: HETEROLOGOUSLY EXPRESSED / Plasmid: PKK 223-3,ACCI-DELETED / Production host: Escherichia coli (E. coli) / Strain (production host): JM 109
References: UniProt: Q16775, hydroxyacylglutathione hydrolase

-
Non-polymers , 6 types, 382 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsONLY THE ARSENIC ATOMS OF CAC A265 AND CAC B265 HAVE BEEN MODELLED. CL 467 TENTATIVELY MODELLED AS ...ONLY THE ARSENIC ATOMS OF CAC A265 AND CAC B265 HAVE BEEN MODELLED. CL 467 TENTATIVELY MODELLED AS A CHLORIDE ION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 29 %
Crystal growpH: 6.5
Details: EQUILABRATION AGAINST 15-30% W/V PEG 2000 MONOMETHYL ETHER 0.2M MG-ACETATE, 0.1M NA-CACODYLATE PH 6.5 AND 2MM DTT
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-30 %(w/v)mPEG20001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoir
42 mMdithiothreitol1reservoir
510 mg/mlprotain1drop
610 mMMOPS1drop
710 mM1dropMgCl2
825 %PEG4001drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.911
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 126060 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4 / % possible all: 99
Reflection
*PLUS
Num. obs: 36838 / Num. measured all: 126060
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.312

-
Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→15 Å / SU B: 3.6 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.17 / Details: VAN DER WAALS RADII ON ZINC IONS SET TO 0.1A
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1799 5 %RANDOM
Rwork0.184 ---
obs0.185 35004 99 %-
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 27 369 4452
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0240.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.912
X-RAY DIFFRACTIONp_mcangle_it1.3542.5
X-RAY DIFFRACTIONp_scbond_it2.7224
X-RAY DIFFRACTIONp_scangle_it3.9126
X-RAY DIFFRACTIONp_plane_restr0.0180.03
X-RAY DIFFRACTIONp_chiral_restr0.090.15
X-RAY DIFFRACTIONp_singtor_nbd0.1660.3
X-RAY DIFFRACTIONp_multtor_nbd0.1620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.17
X-RAY DIFFRACTIONp_staggered_tor14.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.15

+
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