[English] 日本語
Yorodumi
- PDB-7xlf: Crystal structure of CH3-THF complex of methylenetetrahydrofolate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xlf
TitleCrystal structure of CH3-THF complex of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6
Components5,10-methylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / CH3-THF oxidation / Non-NADH/NAD+ binding type / TIM barrel / FLAVOPROTEIN
Function / homology
Function and homology information


methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / cytosol
Similarity search - Function
Methylenetetrahydrofolate reductase-like / Methylenetetrahydrofolate reductase / TIM Barrel - #220 / FAD-linked oxidoreductase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / 5,10-methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesSphingobium sp. SYK-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYu, H.Y. / Senda, M. / Senda, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101001 Japan
CitationJournal: To Be Published
Title: Crystal structural of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6
Authors: Yu, H.Y. / Senda, T.
History
DepositionApr 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: 5,10-methylenetetrahydrofolate reductase
B: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5349
Polymers62,7262
Non-polymers2,8087
Water7,008389
1
A: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7144
Polymers31,3631
Non-polymers1,3513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8205
Polymers31,3631
Non-polymers1,4574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.127, 170.347, 45.151
Angle α, β, γ (deg.)90.000, 104.548, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein 5,10-methylenetetrahydrofolate reductase


Mass: 31362.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Strain: NBRC 103272 / SYK-6 / Gene: metF, SLG_12750 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G2IQS8, 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-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N7O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 20% (w/v) PEG 4000, 0.1 M sodium citrate pH 4.5

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→43.7 Å / Num. obs: 46088 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.064 / Net I/σ(I): 14.3
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 0.853 / Num. unique obs: 2827 / CC1/2: 0.727 / Rpim(I) all: 0.537

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XG9

7xg9


Resolution: 1.85→38.88 Å / SU ML: 0.229 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 2341 5.09 %
Rwork0.1806 43682 -
obs0.1825 46023 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.82 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4207 0 175 389 4771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714498
X-RAY DIFFRACTIONf_angle_d0.92686138
X-RAY DIFFRACTIONf_chiral_restr0.0585691
X-RAY DIFFRACTIONf_plane_restr0.0066779
X-RAY DIFFRACTIONf_dihedral_angle_d13.35241651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.32851380.26122567X-RAY DIFFRACTION99.96
1.89-1.930.33191370.25582518X-RAY DIFFRACTION99.66
1.93-1.970.29311430.22392591X-RAY DIFFRACTION99.89
1.97-2.020.27621400.20882554X-RAY DIFFRACTION100
2.02-2.080.26331360.20022557X-RAY DIFFRACTION99.85
2.08-2.140.24581330.19422567X-RAY DIFFRACTION99.96
2.14-2.210.25291290.18282584X-RAY DIFFRACTION100
2.21-2.290.25511310.20162557X-RAY DIFFRACTION99.63
2.29-2.380.22141130.19332605X-RAY DIFFRACTION100
2.38-2.490.26981410.19342573X-RAY DIFFRACTION100
2.49-2.620.2391380.19912563X-RAY DIFFRACTION100
2.62-2.780.20711420.19982549X-RAY DIFFRACTION99.96
2.78-30.26231490.20442578X-RAY DIFFRACTION99.93
3-3.30.20961450.18652566X-RAY DIFFRACTION100
3.3-3.770.18921440.15872589X-RAY DIFFRACTION99.89
3.77-4.750.14911420.13142554X-RAY DIFFRACTION99.89
4.75-38.880.16171400.14532610X-RAY DIFFRACTION99.82

+
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