[English] 日本語
Yorodumi
- PDB-3bq6: Crystal Structure of T. maritima Cobalamin-Independent Methionine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bq6
TitleCrystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ (Monoclinic)
Components5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
KeywordsTRANSFERASE / MetE / TIM BARREL / HOMOCYSTEINE / ZINC / ZINC INVERSION / Amino-acid biosynthesis / Metal-binding / Methionine biosynthesis / Methyltransferase
Function / homology
Function and homology information


5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / 'de novo' L-methionine biosynthetic process / methylation / zinc ion binding
Similarity search - Function
Cobalamin-independent methionine synthase / Cobalamin-independent methionine synthase MetE, N-terminal / Cobalamin-independent synthase, N-terminal domain / Cobalamin-independent methionine synthase MetE, C-terminal/archaeal / Cobalamin-independent synthase, Catalytic domain / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPejchal, R. / Smith, J.L. / Ludwig, M.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Metal active site elasticity linked to activation of homocysteine in methionine synthases.
Authors: Koutmos, M. / Pejchal, R. / Bomer, T.M. / Matthews, R.G. / Smith, J.L. / Ludwig, M.L.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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: 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
B: 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,9514
Polymers178,8212
Non-polymers1312
Water4,053225
1
A: 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4762
Polymers89,4101
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4762
Polymers89,4101
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.087, 107.604, 107.442
Angle α, β, γ (deg.)90.00, 110.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase / Methionine synthase / vitamin-B12 independent isozyme / Cobalamin-independent methionine synthase


Mass: 89410.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: metE / Plasmid: pET-151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3)
References: UniProt: Q9X112, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 295 K / Method: vapor batch, under oil / pH: 8.5
Details: 19.5% PEG 3350, 0.2M magnesium acetate, 2.5% ethylene glycol, 0.1M Tris-HCl, pH 8.5, VAPOR BATCH, UNDER OIL, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2006
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→48.9 Å / Num. all: 89790 / Num. obs: 89746 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.81 Å2
Reflection shellResolution: 2.1→2.21 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T7L

1t7l


Resolution: 2.1→48.9 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 2244 2.5 %RANDOM
Rwork0.2099 ---
obs0.2106 89746 99.9 %-
all-89790 --
Displacement parametersBiso mean: 39.12 Å2
Baniso -1Baniso -2Baniso -3
1-8.037 Å20 Å2-3.953 Å2
2---7.881 Å20 Å2
3----0.156 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11003 0 2 225 11230
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfOND0.005
X-RAY DIFFRACTIONfNGLE0.845
X-RAY DIFFRACTIONfHIRALITY0.056
X-RAY DIFFRACTIONfLANARITY0.003
X-RAY DIFFRACTIONfIHEDRAL15.048
LS refinement shellResolution: 2.1→2.145 Å
RfactorNum. reflection% reflection
Rfree0.316 139 -
Rwork0.263 --
obs-5569 100 %

+
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