[English] 日本語
Yorodumi
- PDB-7th5: Thermus thermophilus methylenetetrahydrofolate reductase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7th5
TitleThermus thermophilus methylenetetrahydrofolate reductase
ComponentsMethylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / TIM barrel / flavin
Function / homology
Function and homology information


methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / cytosol
Similarity search - Function
5,10-methylenetetrahydrofolate reductase / Methylenetetrahydrofolate reductase-like / Methylenetetrahydrofolate reductase / FAD-linked oxidoreductase-like
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsYamada, K. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: 5-Formyltetrahydrofolate promotes conformational remodeling in a methylenetetrahydrofolate reductase active site and inhibits its activity.
Authors: Yamada, K. / Mendoza, J. / Koutmos, M.
History
DepositionJan 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methylenetetrahydrofolate reductase
B: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7196
Polymers66,1022
Non-polymers1,6174
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion column chromatography with the multi-angle light scattering detector (Igari et al, PLoS (2011))
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-52 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.496, 91.288, 130.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Methylenetetrahydrofolate reductase


Mass: 33050.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHA0327 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SLG6, methylenetetrahydrofolate reductase [NAD(P)H]
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5, 3M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.09→47.07 Å / Num. obs: 42742 / % possible obs: 98.7 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.069 / Rrim(I) all: 0.138 / Net I/σ(I): 7.6
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.621 / Num. unique obs: 2924 / CC1/2: 0.674 / Rpim(I) all: 0.316 / Rrim(I) all: 0.621 / % possible all: 88.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3APY

3apy


Resolution: 2.09→47.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.074 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 2157 5.1 %RANDOM
Rwork0.1817 ---
obs0.1838 40515 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 218.89 Å2 / Biso mean: 34.665 Å2 / Biso min: 10.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å2-0 Å20 Å2
2--1.27 Å2-0 Å2
3----2.12 Å2
Refinement stepCycle: final / Resolution: 2.09→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 160 156 4863
Biso mean--34.39 36.36 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174551
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.6466470
X-RAY DIFFRACTIONr_angle_other_deg0.5321.55810439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.43319.357280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0615774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4271557
X-RAY DIFFRACTIONr_chiral_restr0.0760.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021165
LS refinement shellResolution: 2.094→2.149 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 139 -
Rwork0.274 2750 -
all-2889 -
obs--91.42 %

+
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://pdbjlvh1.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