[English] 日本語
Yorodumi
- PDB-7qbt: B12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qbt
TitleB12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, and S-methyl-5'-thioadenosine bound.
ComponentsMethyl coenzyme M reductase-arginine methyltransferase Mmp10
KeywordsMETAL BINDING PROTEIN / Radical SAM / B12 binding / methyltransferase / sp3 carbon methylation
Function / homology
Function and homology information


iron-sulfur cluster binding / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Radical SAM methyltransferase MA_4551-like / Putative radical SAM, N-terminal / Radical SAM-like domain / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
CO-METHYLCOBALAMIN / : / 5'-DEOXY-5'-METHYLTHIOADENOSINE / IRON/SULFUR CLUSTER / Methyl coenzyme M reductase-arginine methyltransferase Mmp10
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFyfe, C.D. / Chavas, L.M.G. / Legrand, P. / Benjdia, A. / Berteau, O.
Funding support France, 2items
OrganizationGrant numberCountry
European Research Council (ERC)617053 France
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0014 France
CitationJournal: Nature / Year: 2022
Title: Crystallographic snapshots of a B 12 -dependent radical SAM methyltransferase.
Authors: Fyfe, C.D. / Bernardo-Garcia, N. / Fradale, L. / Grimaldi, S. / Guillot, A. / Brewee, C. / Chavas, L.M.G. / Legrand, P. / Benjdia, A. / Berteau, O.
History
DepositionNov 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: 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: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
B: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
C: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
D: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,14824
Polymers191,8594
Non-polymers8,28920
Water22,8431268
1
A: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0376
Polymers47,9651
Non-polymers2,0725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0376
Polymers47,9651
Non-polymers2,0725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0376
Polymers47,9651
Non-polymers2,0725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0376
Polymers47,9651
Non-polymers2,0725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.064, 163.915, 77.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Methyl coenzyme M reductase-arginine methyltransferase Mmp10


Mass: 47964.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: mmp10, HA338_00275 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A832SFM5, Transferases; Transferring one-carbon groups; Methyltransferases

-
Non-polymers , 6 types, 1288 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C63H91CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1268 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG8000, 100 mM Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2021
RadiationMonochromator: Si(111) single-crystal channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→45.72 Å / Num. obs: 137077 / % possible obs: 99.8 % / Redundancy: 13.8 % / Biso Wilson estimate: 37.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.031 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2742 / CC1/2: 0.512 / Rpim(I) all: 0.847 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (16-JUL-2021)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QBS

7qbs


Resolution: 1.9→44.71 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 6765 4.94 %RANDOM
Rwork0.203 ---
obs0.2026 137077 87 %-
Displacement parametersBiso mean: 44.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.3861 Å20 Å20 Å2
2--2.1619 Å20 Å2
3----1.7758 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.9→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12603 0 488 1268 14359
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913410HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1918316HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4810SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2308HARMONIC5
X-RAY DIFFRACTIONt_it13410HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion15.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1790SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11756SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.92 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2856 147 5.36 %
Rwork0.2971 2595 -
all0.2964 2742 -
obs--49.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.30950.3527-0.25780.6307-0.02250.6493-0.0396-0.0251-0.0182-0.0721-0.00490.0723-0.00020.18440.0445-0.0407-0.04590.00020.0095-0.0002-0.0395-50.4545-18.2957-62.6015
20.1903-0.1828-0.4330.28010.20520.94520.11680.0108-0.0741-0.0067-0.12830.1151-0.12430.05180.01140.003-0.05540.0753-0.0213-0.052-0.0161-60.0937-8.3264-39.5519
30.57940.1478-0.37020.37140.56420.8144-0.04520.0567-0-0.00890.03760.04470.04210.09210.0075-0.0384-0.01610.0153-0.0168-0.0321-0.0294-50.0695-60.3469-20.8584
40.41270.0199-0.5980.98510.29920.720.0238-0.06850.01260.0978-0.03940.29230.02520.17010.0156-0.0266-0.00330.0673-0.0302-0.0760.0398-59.6334-52.35042.7935
51.414-0.0738-1.13350.2666-0.90371.61580.197-0.109-0.03290.0326-0.0302-0.05610.0159-0.0708-0.1668-0.0435-0.05340.04530.07590.0443-0.0894-23.2474-18.6201-18.0635
60.760.7449-0.47250.8415-0.77831.6197-0.01320.2927-0.04020.17330.0354-0.1710.135-0.2054-0.0222-0.14360.01580.04860.08340.1346-0.0373-14.9759-10.2442-42.2312
70.5381-0.2053-0.19750.40760.140.5821-0.0176-0.0190.00440.028-0.0248-0.10290.0348-0.16580.0424-0.05330.0333-0.01680.01350.0191-0.0375-22.3302-57.526-53.7899
80.1670.3329-0.14760.0975-0.31380.81040.01170.1212-0.04920.116-0.1025-0.0611-0.0975-0.05620.0908-0.02520.04180.030.03120.0914-0.0243-13.6204-47.0108-76.8905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|257 A|502 - A|503 }
2X-RAY DIFFRACTION2{ A|258 - A|501 A|504 }
3X-RAY DIFFRACTION3{ B|1 - B|257 B|502 - B|503 }
4X-RAY DIFFRACTION4{ B|258 - B|501 B|504 }
5X-RAY DIFFRACTION5{ C|2 - C|257 C|502 - C|503 }
6X-RAY DIFFRACTION6{ C|258 - C|501 C|504 }
7X-RAY DIFFRACTION7{ D|1 - D|257 D|502 - D|503 }
8X-RAY DIFFRACTION8{ D|258 - D|501 D|504 }

+
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