[English] 日本語
Yorodumi
- PDB-2p18: Crystal structure of the Leishmania infantum glyoxalase II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p18
TitleCrystal structure of the Leishmania infantum glyoxalase II
ComponentsGlyoxalase II
KeywordsHYDROLASE / metalloprotein / beta sandwich / alpha-helical domain
Function / homology
Function and homology information


hydroxyacylglutathione hydrolase / hydroxyacylglutathione hydrolase activity / metal ion binding
Similarity search - Function
Hydroxyacylglutathione hydrolase, C-terminal domain / Hydroxyacylglutathione hydrolase, MBL domain / Hydroxyacylglutathione hydrolase C-terminus / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / SPERMIDINE / Putative glyoxalase II
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTrincao, J. / Barata, L. / Najmudin, S. / Bonifacio, C. / Romao, M.J.
CitationJournal: Biochemistry / Year: 2008
Title: Catalysis and Structural Properties of Leishmania infantum Glyoxalase II: Trypanothione Specificity and Phylogeny.
Authors: Silva, M.S. / Barata, L. / Ferreira, A.E. / Romao, S. / Tomas, A.M. / Freire, A.P. / Cordeiro, C.
History
DepositionMar 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / 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 / _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: Glyoxalase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7595
Polymers34,4231
Non-polymers3364
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.705, 88.989, 85.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1033-

HOH

-
Components

#1: Protein Glyoxalase II


Mass: 34422.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: GLO2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus
References: UniProt: Q2PYN0, hydroxyacylglutathione hydrolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.85 Å3/Da / Density % sol: 33.52 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 4K, 0.2M MgCl2, 0.1M Ammonium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9538
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2006 / Details: Undulator
RadiationMonochromator: Si(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 1.8→53.376 Å / Num. all: 23962 / Num. obs: 23962 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 6.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.6 / Num. measured all: 20168 / Num. unique all: 3459 / Rsym value: 0.468 / % possible all: 100

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å25.89 Å
Translation2.7 Å25.89 Å

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MxCuBEdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QH3

1qh3


Resolution: 1.8→53.38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.535 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1224 5.1 %RANDOM
Rwork0.171 ---
all0.246 23955 --
obs0.172 23955 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.921 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→53.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 16 111 2303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212261
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9393070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.7595284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45323.883103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01915344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0421510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021744
X-RAY DIFFRACTIONr_nbd_refined0.2090.21117
X-RAY DIFFRACTIONr_nbtor_refined0.310.21532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2121
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.29
X-RAY DIFFRACTIONr_mcbond_it0.9871.51454
X-RAY DIFFRACTIONr_mcangle_it1.00922277
X-RAY DIFFRACTIONr_scbond_it2.1233903
X-RAY DIFFRACTIONr_scangle_it2.9544.5792
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 95 -
Rwork0.235 1653 -
obs-1748 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.22831.09521.07512.9543-0.33711.8364-0.0334-0.59590.24830.5208-0.1064-0.1091-0.094-0.00140.1398-0.0143-0.01070.0090.0175-0.0655-0.103921.07633.74161.595
220.6579.53329.03713.84564.6028.72240.0688-1.75980.92940.6675-0.1972-0.1009-0.5422-0.26910.12840.16090.00230.12810.3084-0.22130.015616.16937.42369.35
34.1394-0.70990.08584.03780.57612.88-0.0918-0.63980.75210.43090.02350.1279-0.2968-0.22920.0683-0.04820.03210.0301-0.0145-0.10030.022510.67336.81456.562
411.2301-3.8784-5.15286.4694-0.79723.2801-0.1246-1.98771.60291.32340.4403-1.1069-2.8536-0.6232-0.31570.4720.1453-0.07860.3371-0.34450.47159.74647.5260.379
51.9109-0.15570.11912.7096-0.18571.37750.0859-0.04690.32560.043-0.061-0.091-0.10430.0349-0.0249-0.1315-0.00330.0299-0.1215-0.0077-0.091519.0833.45447.124
618.23216.58483.92256.47141.82194.00970.01290.8293-0.0397-0.54980.07780.0819-0.0467-0.0435-0.0907-0.06650.0629-0.0114-0.04980.0024-0.17320.26922.24137.713
72.93910.1463-0.40492.82680.34331.2030.0475-0.0743-0.20980.0754-0.039-0.23170.11470.0762-0.0085-0.11840.0156-0.028-0.08850.0216-0.136328.71720.75149.342
89.1725-5.8029-8.42587.937.039111.3985-0.2248-0.3517-0.37010.82420.0646-0.22750.54930.2850.16030.02360.033-0.09370.00540.0986-0.061131.91911.54957.132
93.9987-0.3481-0.33671.97541.06634.14720.09960.2015-0.38840.08050.0446-0.07020.17790.242-0.1442-0.11890.0185-0.0381-0.11370.0108-0.096428.47516.18745.995
1018.0340.2333-7.05817.50544.78869.19220.10630.4526-1.42940.4391-0.30450.59280.6171-0.36720.1982-0.02110.0018-0.067-0.0546-0.04780.036919.0599.89440.489
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 4517 - 61
2246 - 5762 - 73
3366 - 9082 - 106
4491 - 103107 - 119
55104 - 177120 - 193
66178 - 189194 - 205
77190 - 226206 - 242
88227 - 247243 - 263
99248 - 284264 - 300
1010285 - 293301 - 309

+
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