[English] 日本語
Yorodumi
- PDB-1f6y: MAD CRYSTAL STRUCTURE ANALYSIS OF METHYLTETRAHYDROFOLATE: CORRINO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f6y
TitleMAD CRYSTAL STRUCTURE ANALYSIS OF METHYLTETRAHYDROFOLATE: CORRINOID/IRON-SULFUR PROTEIN METHYLTRANSFERASE (METR)
Components5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
KeywordsTRANSFERASE / carbon dioxide fixation / cobalamin / methyltatrahydrofolate / methyltransferase / one-carbon metabolism / TIM barrel / homodimer
Function / homology
Function and homology information


5-methyltetrahydrofolate-corrinoid/iron-sulfur protein Co-methyltransferase / methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity / pteridine-containing compound metabolic process / methionine synthase activity / carbon fixation / cobalamin binding / 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-methyltetrahydrofolate:corrinoid/iron-sulfur protein co-methyltransferase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 2.2 Å
AuthorsDoukov, T.I. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase.
Authors: Doukov, T. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Preliminary X-ray Crystallographic Study of Methyltetrahydrofolate: Corrinoid/Iron-Sulfur Protein Methyltransferase from Clostridium thermoaceticum
Authors: Doukov, T.I. / Zhao, S. / Ross II, C.R. / Roberts, D.L. / Kim, J.J. / Ragsdale, S.W. / Stezowski, J.J.
#2: Journal: J.BACTERIOL. / Year: 1994
Title: The Reductive Acetyl Coenzyme A Pathway: Sequence and Heterologous Expression of Active Methyltetrahydrofolate:Corrinoid/Iron-Sulfur Protein Methyltransferase from Clostridium thermoaceticum
Authors: Roberts, D.L. / Zhao, S. / Doukov, T. / Ragsdale, S.W.
#3: Journal: Biochemistry / Year: 1999
Title: Binding of (6R,S)-Methyltetrahydrofolate to Methyltransferase from Clostridium thermoaceticum: Role of Protonation of Methyltetrahydrofolate in the Mechanism of Methyl Transfer
Authors: Seravalli, J. / Shoemaker, R.K. / Sudbeck, M.L. / Ragsdale, S.W.
#4: Journal: Biochemistry / Year: 1999
Title: Mechanism of Transfer of the Methyl Group from (6S)-Methyltetrahydrofolate to the Corrinoid/Iron-Sulfur Protein Catalyzed by the Methyltransferase from Clostridium thermoaceticum: A Key Step ...Title: Mechanism of Transfer of the Methyl Group from (6S)-Methyltetrahydrofolate to the Corrinoid/Iron-Sulfur Protein Catalyzed by the Methyltransferase from Clostridium thermoaceticum: A Key Step in the Wood-Ljungdahl Pathway of Acetyl-CoA Synthesis
Authors: Seravalli, J. / Zhao, S. / Ragsdale, S.W.
History
DepositionJun 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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


Theoretical massNumber of molelcules
Total (without water)57,3402
Polymers57,3402
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-24 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.000, 89.412, 115.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE


Mass: 28670.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Strain: ATCC 39073 / Cellular location: CYTOPLASMIC / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q46389
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9-15% PEGmme 5000, 20% Glycerol, 50 mM HEPES pH 7.5, 20-50 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
pH: 7.6 / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMdithiothreitol1drop
250 mMTris1drop
310 mM1dropNaCl
420 mg/mlprotein1drop
59-15 %(w/v)PEGmme50001reservoir
620-50 mM1reservoirCaCl2
720 %glycerol1reservoir
850 mMHEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→7 Å / Num. all: 34455 / Num. obs: 28189 / % possible obs: 81.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.7
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.294 / % possible all: 87.6

-
Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 2.2→7 Å / Num. parameters: 1650 / Num. restraintsaints: 1601 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 291 10 %Thin sliced (SHELX97)
Rwork0.2012 ---
all0.209 34455 --
obs0.206 28189 81.8 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4125
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 0 185 4125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.01
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.2306 / Rfactor Rwork: 0.2064
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_plane_restr0.031

+
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