[English] 日本語
Yorodumi
- PDB-8bgr: FAD-independent Methylene-Tetrahydrofolate Reductase from Mycobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bgr
TitleFAD-independent Methylene-Tetrahydrofolate Reductase from Mycobacterium hassiacum
ComponentsMethylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / FAD-independent / NADH-dependent / Methylene-Tetrahydrofolate Reductase
Function / homology: / Mycobacterial methylenetetrahydrofolate reductase / TIM Barrel - #220 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesMycolicibacterium hassiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGehl, M. / Ermler, U. / Shima, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Proteins / Year: 2023
Title: Crystal structure of FAD-independent methylene-tetrahydrofolate reductase from Mycobacterium hassiacum.
Authors: Gehl, M. / Demmer, U. / Ermler, U. / Shima, S.
History
DepositionOct 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methylenetetrahydrofolate reductase


Theoretical massNumber of molelcules
Total (without water)32,8381
Polymers32,8381
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.790, 45.790, 257.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Methylenetetrahydrofolate reductase


Mass: 32837.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium hassiacum (bacteria) / Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: C731_4202, MHAS_04356 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K5BDY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 26845 / % possible obs: 94.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 25.93 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.104 / Rsym value: 0.093 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3422 / CC1/2: 0.851 / Rrim(I) all: 1.3 / Rsym value: 1.11

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold Model

Resolution: 1.8→37.31 Å / SU ML: 0.2736 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.7791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 1216 4.79 %
Rwork0.2322 24157 -
obs0.2331 25373 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 0 206 2452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272333
X-RAY DIFFRACTIONf_angle_d0.5973172
X-RAY DIFFRACTIONf_chiral_restr0.0431351
X-RAY DIFFRACTIONf_plane_restr0.0038423
X-RAY DIFFRACTIONf_dihedral_angle_d12.3688883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.39321260.34732380X-RAY DIFFRACTION87.81
1.87-1.960.29831330.32272464X-RAY DIFFRACTION89.58
1.96-2.060.35111120.2952564X-RAY DIFFRACTION92.4
2.06-2.190.30741250.27262636X-RAY DIFFRACTION94.04
2.19-2.360.29241410.2742662X-RAY DIFFRACTION96.42
2.36-2.60.30991480.26172751X-RAY DIFFRACTION98.17
2.6-2.970.30641490.252792X-RAY DIFFRACTION98.72
2.97-3.740.2611240.21012864X-RAY DIFFRACTION98.48
3.74-37.310.16421580.18773044X-RAY DIFFRACTION98.25

+
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