[English] 日本語
Yorodumi
- PDB-1b93: METHYLGLYOXAL SYNTHASE FROM ESCHERICHIA COLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b93
TitleMETHYLGLYOXAL SYNTHASE FROM ESCHERICHIA COLI
ComponentsPROTEIN (METHYLGLYOXAL 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
FORMIC ACID / PHOSPHATE ION / Methylglyoxal synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.9 Å
AuthorsSaadat, D. / Harrison, D.H.T.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of methylglyoxal synthase from Escherichia coli.
Authors: Saadat, D. / Harrison, D.H.
History
DepositionFeb 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: 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 / 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: PROTEIN (METHYLGLYOXAL SYNTHASE)
B: PROTEIN (METHYLGLYOXAL SYNTHASE)
C: PROTEIN (METHYLGLYOXAL SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,23011
Polymers50,8133
Non-polymers4178
Water3,909217
1
A: PROTEIN (METHYLGLYOXAL SYNTHASE)
B: PROTEIN (METHYLGLYOXAL SYNTHASE)
C: PROTEIN (METHYLGLYOXAL SYNTHASE)
hetero molecules

A: PROTEIN (METHYLGLYOXAL SYNTHASE)
B: PROTEIN (METHYLGLYOXAL SYNTHASE)
C: PROTEIN (METHYLGLYOXAL SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,46022
Polymers101,6256
Non-polymers83416
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area18850 Å2
ΔGint-156 kcal/mol
Surface area30230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.340, 123.340, 155.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.187058, 0.174494, 0.966727), (0.906715, 0.409333, 0.101561), (-0.377992, 0.895543, -0.234785)
Vector: -75.202, 8.4686, 65.8311)

-
Components

#1: Protein PROTEIN (METHYLGLYOXAL SYNTHASE)


Mass: 16937.545 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: LE392 / Cellular location: CYTOPLASM / Gene: MGSA / Plasmid: PETMGSWT / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): MGSA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A731, methylglyoxal synthase
#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.48 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMTris-acetate1drop
31 mM1dropKH2PO4
41.2 Msodium formate1reservoir
5100 mMsodium cacodylate1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 58374 / % possible obs: 89.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077
Reflection shellResolution: 1.8→1.88 Å / % possible all: 36.8
Reflection
*PLUS
Num. measured all: 247774
Reflection shell
*PLUS
% possible obs: 36.8 %

-
Processing

Software
NameVersionClassification
XTALVIEWrefinement
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3788 7.1 %RANDOM
Rwork0.181 ---
obs0.181 53546 82.1 %-
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 26 217 3639
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.451.5
X-RAY DIFFRACTIONx_mcangle_it2.282
X-RAY DIFFRACTIONx_scbond_it2.982
X-RAY DIFFRACTIONx_scangle_it4.522.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 335 7.4 %
Rwork0.281 4163 -
obs--42.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPPAR2:FMT.PARTOPH19.SOL
X-RAY DIFFRACTION3TOPPAR2:PO4.PARTOPPAR2:FMT.TOP
X-RAY DIFFRACTION4TOPPAR2:PO4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65

+
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