[English] 日本語
Yorodumi
- PDB-2e7f: 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltran... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2e7f
Title5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase complexed with methyltetrahydrofolate to 2.2 Angsrom resolution
Components5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
KeywordsTRANSFERASE / Methyltetrahydrofolate-protein complex / corrionoid / vitamin B12 / TIM Barrel
Function / homology
Function and homology information


5-methyltetrahydrofolate-corrinoid/iron-sulfur protein Co-methyltransferase / methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity / methionine synthase activity / homocysteine metabolic process / carbon fixation / cobalamin binding / tetrahydrofolate metabolic process / methyltransferase activity / methylation / calcium ion binding / cytosol
Similarity search - Function
: / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / 5-methyltetrahydrofolate:corrinoid/iron-sulfur protein co-methyltransferase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDoukov, T.I. / Drennan, C.L. / Hemmi, H. / Ragsdale, S.W.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structural and kinetic evidence for an extended hydrogen-bonding network in catalysis of methyl group transfer. Role of an active site asparagine residue in activation of methyl transfer by methyltransferases.
Authors: Doukov, T.I. / Hemmi, H. / Drennan, C.L. / Ragsdale, S.W.
#1: Journal: Structure / Year: 2000
Title: Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase
Authors: Doukov, T.I. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W.
History
DepositionJan 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
B: 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2756
Polymers57,2762
Non-polymers9994
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-43 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.159, 78.547, 135.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S)

-
Components

#1: Protein 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase


Mass: 28638.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Gene: MeTr, acsE / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS(met-) / References: UniProt: Q46389
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8-15% PEGmme 5000, 0.05M Calcium acetate, 20% Glycerol, 0.05M HEPES buffer; 3-fold molar excess of the MTHF substrate (Schricks Labolatories, Jona, Switzerland). The supersaturation of the ...Details: 8-15% PEGmme 5000, 0.05M Calcium acetate, 20% Glycerol, 0.05M HEPES buffer; 3-fold molar excess of the MTHF substrate (Schricks Labolatories, Jona, Switzerland). The supersaturation of the precipitant solution required dilution of the protein-CH3-H4folate complex by 50-100-fold in order to obtain single crystals., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.91938 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 30, 2000
RadiationMonochromator: SI(111) or SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91938 Å / Relative weight: 1
ReflectionResolution: 2.2→30.92 Å / Num. obs: 26806 / % possible obs: 96.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 1750 / Rsym value: 0.206 / % possible all: 87.9

-
Processing

Software
NameVersionClassification
CBASSdata collection
EPMRphasing
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F6Y

1f6y


Resolution: 2.2→30.88 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2586 -RANDOM
Rwork0.172 ---
obs0.178 24177 96.04 %-
all-26763 --
Refinement stepCycle: LAST / Resolution: 2.2→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 68 435 4497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.018
LS refinement shellResolution: 2.2→2.26 Å
RfactorNum. reflection% reflection
Rfree0.245 165 -
Rwork0.193 --
obs-1571 85.77 %

+
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