[English] 日本語
Yorodumi
- PDB-1qin: HUMAN GLYOXALASE I COMPLEXED WITH S-(N-HYDROXY-N-P-IODOPHENYLCARB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qin
TitleHUMAN GLYOXALASE I COMPLEXED WITH S-(N-HYDROXY-N-P-IODOPHENYLCARBAMOYL) GLUTATHIONE
ComponentsPROTEIN (LACTOYLGLUTATHIONE LYASE)
KeywordsLYASE / LACTOYLGLUTATHIONE LYASE / GLYOXALASE I
Function / homology
Function and homology information


lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / extracellular exosome ...lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytoplasm / 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
S-(N-HYDROXY-N-IODOPHENYLCARBAMOYL)GLUTATHIONE / Lactoylglutathione lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 Å
AuthorsCameron, A.D. / Ridderstrom, M. / Olin, B. / Mannervik, B.
CitationJournal: Biochemistry / Year: 1999
Title: Reaction mechanism of glyoxalase I explored by an X-ray crystallographic analysis of the human enzyme in complex with a transition state analogue.
Authors: Cameron, A.D. / Ridderstrom, M. / Olin, B. / Kavarana, M.J. / Creighton, D.J. / Mannervik, B.
History
DepositionJun 14, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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 (LACTOYLGLUTATHIONE LYASE)
B: PROTEIN (LACTOYLGLUTATHIONE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6176
Polymers41,3452
Non-polymers1,2724
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-150 kcal/mol
Surface area15310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.700, 54.500, 78.900
Angle α, β, γ (deg.)90.00, 98.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9898, -0.12358, 0.07082), (-0.12169, 0.47539, -0.87132), (0.07402, -0.87105, -0.48558)
Vector: -4.85506, 17.46366, 30.28586)

-
Components

#1: Protein PROTEIN (LACTOYLGLUTATHIONE LYASE) / GLYOXALASE I


Mass: 20672.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HETEROLOGOUSLY EXPRESSED / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 103 / References: UniProt: Q04760, 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-GIP / S-(N-HYDROXY-N-IODOPHENYLCARBAMOYL)GLUTATHIONE


Mass: 570.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23IN4O8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE REFERENCE FOR THE SEQUENCE: M.RIDDERSTROM, B.MANNERVIK, BIOCHEM J. 314, 463-467, 1996.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 49 %
Crystal growpH: 5.8
Details: PROTEIN WAS CRYSTALLISED BY EQILLABRATION AGAINST PEG 2000 MONOMETHLY ETHER, 50 MM MES PH 5.8, 0.1M NACL. HIPC-GSH WAS PRESENT IN THE PROTEIN SOLUTION
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / Details: Cameron, A.D., (1997) EMBO J., 16, 3386.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.5-15 %(w/v)PEG20001drop
225 mMMES1drop
30.05 M1dropNaCl
46 mg/mlprotein1drop
50.5 %2-mercaptoethanol1drop
61 mMS-benzyl-glutathione1drop
725-30 %(w/v)PEG20001reservoir
850 mMMES1reservoir
90.1 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 3, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→29 Å / Num. obs: 28148 / % possible obs: 93.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.83 / Net I/σ(I): 9
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3.2 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 49286
Reflection shell
*PLUS
% possible obs: 93.5 %

-
Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: OTHER / Resolution: 2→29 Å / SU B: 3.3 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1418 5 %RANDOM
Rwork0.178 ---
obs0.18 28134 94 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 64 191 3055
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_d0.0230.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9532
X-RAY DIFFRACTIONp_mcangle_it1.5122.5
X-RAY DIFFRACTIONp_scbond_it3.1054
X-RAY DIFFRACTIONp_scangle_it4.6126
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.090.15
X-RAY DIFFRACTIONp_singtor_nbd0.1690.3
X-RAY DIFFRACTIONp_multtor_nbd0.230.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.57
X-RAY DIFFRACTIONp_staggered_tor15.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 29 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.090.15

+
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