[English] 日本語
Yorodumi
- PDB-7xcn: Crystal structure of the MttB-MttC complex at 2.7 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xcn
TitleCrystal structure of the MttB-MttC complex at 2.7 A resolution
Components
  • Trimethylamine methyltransferase
  • Trimethylamine methyltransferase corrinoid protein
KeywordsTRANSFERASE / pyrrolysine / trimethylamine / methyltransferase / corrinoid protein
Function / homology
Function and homology information


trimethylamine-corrinoid protein Co-methyltransferase / trimethylamine methyltransferase activity / methanogenesis / cobalamin binding / cobalt ion binding / methyltransferase activity / methylation
Similarity search - Function
Trimethylamine methyltransferase, Methanosarcina / Methyltransferase cognate corrinoid protein / Trimethylamine methyltransferase / MttB-like superfamily / Trimethylamine methyltransferase (MTTB) / Methionine synthase domain / B12-binding N-terminal domain profile. / B12 binding domain / Cobalamin-binding domain / : ...Trimethylamine methyltransferase, Methanosarcina / Methyltransferase cognate corrinoid protein / Trimethylamine methyltransferase / MttB-like superfamily / Trimethylamine methyltransferase (MTTB) / Methionine synthase domain / B12-binding N-terminal domain profile. / B12 binding domain / Cobalamin-binding domain / : / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5-HYDROXYBENZIMIDAZOLYLCOBAMIDE / Trimethylamine methyltransferase corrinoid protein / Trimethylamine methyltransferase
Similarity search - Component
Biological speciesMethanosarcina barkeri MS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, J. / Chan, M.K.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14116620 Hong Kong
CitationJournal: Commun Biol / Year: 2023
Title: Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex.
Authors: Li, J. / Kang, P.T. / Jiang, R. / Lee, J.Y. / Soares, J.A. / Krzycki, J.A. / Chan, M.K.
History
DepositionMar 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 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: Trimethylamine methyltransferase
B: Trimethylamine methyltransferase
C: Trimethylamine methyltransferase
D: Trimethylamine methyltransferase
E: Trimethylamine methyltransferase
F: Trimethylamine methyltransferase
M: Trimethylamine methyltransferase corrinoid protein
N: Trimethylamine methyltransferase corrinoid protein
O: Trimethylamine methyltransferase corrinoid protein
P: Trimethylamine methyltransferase corrinoid protein
Q: Trimethylamine methyltransferase corrinoid protein
R: Trimethylamine methyltransferase corrinoid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,85422
Polymers472,58212
Non-polymers8,27210
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area76550 Å2
ΔGint-480 kcal/mol
Surface area131410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.434, 188.138, 123.952
Angle α, β, γ (deg.)90.000, 119.250, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Trimethylamine methyltransferase


Mass: 54854.504 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina barkeri MS (archaea) / Gene: MSBRM_0461 / Production host: Methanosarcina acetivorans C2A (archaea)
References: UniProt: A0A0E3QRM4, trimethylamine-corrinoid protein Co-methyltransferase
#2: Protein
Trimethylamine methyltransferase corrinoid protein


Mass: 23909.213 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina barkeri MS (archaea) / Gene: MSBRM_0460 / Production host: Methanosarcina acetivorans C2A (archaea) / References: UniProt: A0A0E3QQC8
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-HCB / 5-HYDROXYBENZIMIDAZOLYLCOBAMIDE


Mass: 1317.294 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C60H84CoN13O15P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 0.5 ul MttB (3 mg/ml in 16mM potassium phosphate buffer pH7.4, 400mM NaCl, 160mM Imidazole, 20% glycerol, 1.6mM DTT) 0.5 ul MttC (10 mg/ml in 40 mM Tris buffer pH7, 200mM NaCl, 20% glycerol) ...Details: 0.5 ul MttB (3 mg/ml in 16mM potassium phosphate buffer pH7.4, 400mM NaCl, 160mM Imidazole, 20% glycerol, 1.6mM DTT) 0.5 ul MttC (10 mg/ml in 40 mM Tris buffer pH7, 200mM NaCl, 20% glycerol) 1 ul reservoir solution (18% PEG 8000, 0.1M citric acid pH 5, 1M LiC)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 132103 / % possible obs: 99.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.049 / Rrim(I) all: 0.092 / Χ2: 0.899 / Net I/σ(I): 9.1 / Num. measured all: 458004
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.40.57466190.730.3640.6820.787100
2.75-2.83.50.46965670.7850.2940.5550.818100
2.8-2.853.50.4465910.7930.2750.520.858100
2.85-2.913.50.37166170.8550.2320.4390.845100
2.91-2.973.50.3166010.8880.1930.3660.849100
2.97-3.043.50.2666010.9130.1620.3070.878100
3.04-3.123.50.22166040.930.1390.2620.91100
3.12-3.23.50.19266020.9460.120.2270.946100
3.2-3.293.50.15466060.9650.0970.1830.94100
3.29-3.43.50.13365730.9680.0840.1580.996100
3.4-3.523.50.11366200.9730.0710.1330.991100
3.52-3.663.50.09666430.9770.0610.1141.01199.9
3.66-3.833.50.08165950.9810.0510.0960.955100
3.83-4.033.40.0766090.9830.0450.0830.93599.9
4.03-4.283.40.06366300.9830.040.0750.89599.8
4.28-4.63.40.05966160.9830.0390.0710.93199.8
4.6-5.063.40.06265690.9820.040.0740.97899.5
5.06-5.773.50.05766320.9820.0360.0670.83799.5
5.77-7.223.50.05365950.9840.0340.0630.76699.2
7.22-203.40.0566130.9820.0330.060.85598.3

-
Processing

Software
NameVersionClassification
CNSrefinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EZX

3ezx


Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2382 10543 8 %
Rwork0.1915 114366 -
obs-124909 95 %
Solvent computationBsol: 29.0846 Å2
Displacement parametersBiso max: 140.31 Å2 / Biso mean: 46.9495 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--0.684 Å20 Å2-1.205 Å2
2--0.463 Å20 Å2
3---0.222 Å2
Refinement stepCycle: final / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32140 0 564 373 33077
Biso mean--55.93 27.11 -
Num. residues----4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.253
X-RAY DIFFRACTIONc_mcbond_it4.7451.5
X-RAY DIFFRACTIONc_scbond_it7.772
X-RAY DIFFRACTIONc_mcangle_it6.6532
X-RAY DIFFRACTIONc_scangle_it9.8362.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)Num. reflection all
2.7-2.80.3151881367.2
2.8-2.910.3227790.26541125586.711334
2.91-3.040.306313090.23571166398.612972
3.04-3.20.302512540.23351183310013087
3.2-3.40.282113220.21531178310013105
3.4-3.660.249513030.18791183899.913141
3.66-4.030.227613220.17191180299.913124
4.03-4.60.202912680.14861185699.813124
4.6-5.770.217613490.16381175299.513101
5.77-200.209913370.17081177198.613108
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6bg5.param
X-RAY DIFFRACTION7HCB_new.par
X-RAY DIFFRACTION8gol.param
X-RAY DIFFRACTION9cis_peptide_cis111.param

+
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