[English] 日本語
Yorodumi
- PDB-1ik4: X-ray Structure of Methylglyoxal Synthase from E. coli Complexed ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ik4
TitleX-ray Structure of Methylglyoxal Synthase from E. coli Complexed with Phosphoglycolohydroxamic Acid
ComponentsMETHYLGLYOXAL SYNTHASE
KeywordsLYASE / GLYCOLYTIC BYPASS / METHYLGLYOXAL
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / protein hexamerization / identical protein binding / cytosol
Similarity search - Function
Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Rossmann fold ...Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOGLYCOLOHYDROXAMIC ACID / Methylglyoxal synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMarks, G.T. / Harris, T.K. / Massiah, M.A. / Mildvan, A.S. / Harrison, D.H.T.
CitationJournal: Biochemistry / Year: 2001
Title: Mechanistic implications of methylglyoxal synthase complexed with phosphoglycolohydroxamic acid as observed by X-ray crystallography and NMR spectroscopy.
Authors: Marks, G.T. / Harris, T.K. / Massiah, M.A. / Mildvan, A.S. / Harrison, D.H.
History
DepositionMay 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: METHYLGLYOXAL SYNTHASE
B: METHYLGLYOXAL SYNTHASE
C: METHYLGLYOXAL SYNTHASE
D: METHYLGLYOXAL SYNTHASE
E: METHYLGLYOXAL SYNTHASE
F: METHYLGLYOXAL SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,65212
Polymers101,6256
Non-polymers1,0266
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20310 Å2
ΔGint-193 kcal/mol
Surface area29590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.05, 129.53, 178.54
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
METHYLGLYOXAL SYNTHASE / / MGS


Mass: 16937.545 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MGSA / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A731, methylglyoxal synthase
#2: Chemical
ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 1500, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG15001reservoir
2100 mMsodium cacodylate1reservoir
325 mMprotein1drop
450 mMimidazole-HCl1drop
51 mMpotassium phosphate1drop
610 mMPGH1drop

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 17, 1999
RadiationMonochromator: Osmic Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 84272 / Num. obs: 84272 / % possible obs: 81.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.284 / % possible all: 51.5
Reflection
*PLUS
Num. measured all: 467479
Reflection shell
*PLUS
% possible obs: 51.5 %

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.206 4685 SHELLS
Rwork0.169 --
all0.266 84272 -
obs0.294 62475 -
Refine analyzeLuzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6968 0 60 400 7428
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 0 / Num. reflection Rfree: 6217 / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.66
LS refinement shell
*PLUS
Rfactor Rfree: 0.3 / Rfactor obs: 0.291

+
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