[English] 日本語
Yorodumi
- PDB-6l0u: Crystal structure of mouse glyoxalase I complexed with a small mo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l0u
TitleCrystal structure of mouse glyoxalase I complexed with a small molecule inhibitor
ComponentsLactoylglutathione lyase
KeywordsLYASE/LYASE INHIBITOR / mouse glyoxalase I / inhibitor / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


Pyruvate metabolism / lactoylglutathione lyase / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / lactoylglutathione lyase activity / 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. / 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
Similarity search - Domain/homology
Chem-E1L / Lactoylglutathione lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJiang, L.L. / Zhou, L.
CitationJournal: To Be Published
Title: Crystal structure of mouse glyoxalase I complexed with a small molecule inhibitor
Authors: Jiang, L.L. / Zhou, L.
History
DepositionSep 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)41,0805
Polymers40,5582
Non-polymers5223
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-129 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.785, 64.635, 65.794
Angle α, β, γ (deg.)90.000, 101.580, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1PROPROchain AAA6 - 1841 - 179
2SERSERchain BBB8 - 1843 - 179

-
Components

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


Mass: 20278.953 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) / 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-E1L / N-[4-(trifluoromethyloxy)phenyl]-1,3,4,9-tetrahydropyrido[3,4-b]indole-2-carbothioamide


Mass: 391.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16F3N3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES pH 6.0, 12% (w/v) PEG2000, 16% v/v 2-Propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 25098 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 0.663 / Net I/σ(I): 5.3 / Num. measured all: 167399
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.95-2.026.20.57225070.8640.2460.6240.433
2.02-2.16.30.43224780.9220.1850.470.469
2.1-2.26.90.31825210.9530.1290.3440.505
2.2-2.316.90.24424780.9690.0990.2640.53
2.31-2.466.50.1825110.9810.0760.1960.576
2.46-2.656.70.14324910.9870.060.1550.629
2.65-2.9170.10324880.9940.0410.1110.74
2.91-3.336.50.07325100.9950.0310.080.872
3.33-4.270.05325340.9980.0210.0570.991
4.2-506.50.04125800.9990.0170.0440.84

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZA0

2za0


Resolution: 1.95→23.16 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.46
RfactorNum. reflection% reflection
Rfree0.2443 1277 5.1 %
Rwork0.1965 --
obs0.1989 25062 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.82 Å2 / Biso mean: 41.79 Å2 / Biso min: 18.66 Å2
Refinement stepCycle: final / Resolution: 1.95→23.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 45 108 2987
Biso mean--56.09 40.12 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082935
X-RAY DIFFRACTIONf_angle_d1.2473974
X-RAY DIFFRACTIONf_chiral_restr0.088424
X-RAY DIFFRACTIONf_plane_restr0.007509
X-RAY DIFFRACTIONf_dihedral_angle_d14.1051093
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1646X-RAY DIFFRACTION8.628TORSIONAL
12B1646X-RAY DIFFRACTION8.628TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.02880.30661490.2449258298
2.0288-2.1210.26781360.23192648100
2.121-2.23280.2471160.21272650100
2.2328-2.37250.26041280.2142639100
2.3725-2.55550.2661600.21182615100
2.5555-2.81230.27031450.21392660100
2.8123-3.21830.24111530.19422638100
3.2183-4.05120.24511410.18632653100
4.0512-23.160.22141490.18232700100

+
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