[English] 日本語
Yorodumi
- PDB-7xcl: Crystal structure of trimethylamine methyltransferase MttB from M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xcl
TitleCrystal structure of trimethylamine methyltransferase MttB from Methanosarcina barkeri at 2.5 A resolution
ComponentsTrimethylamine methyltransferase
KeywordsTRANSFERASE / pyrrolysine / trimethylamine / methyltransferase / corrinoid protein
Function / homologytrimethylamine-corrinoid protein Co-methyltransferase / trimethylamine methyltransferase activity / Trimethylamine methyltransferase, Methanosarcina / Trimethylamine methyltransferase / MttB-like superfamily / Trimethylamine methyltransferase (MTTB) / methanogenesis / methylation / Trimethylamine methyltransferase
Function and homology information
Biological speciesMethanosarcina barkeri MS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,27823
Polymers329,1276
Non-polymers1,15117
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51670 Å2
ΔGint-364 kcal/mol
Surface area88740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.492, 175.492, 300.996
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 4.15 Å3/Da / Density % sol: 70.35 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 1 ul protein (8 mg/mL MttB in 20 mM potassium phosphate buffer pH 7.4, 500 mM NaCl, 240 mM imidazole, 20% glycerol), 1 ul reservoir (4% MPD, 0.1 M citric acid pH 4.5) solutions

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99984 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 172408 / % possible obs: 93.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Χ2: 1.058 / Net I/σ(I): 7 / Num. measured all: 932353
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5450.88683760.7470.4090.9820.62692.1
2.54-2.5950.70784020.810.3240.7820.64692.6
2.59-2.6450.61485320.8380.2810.680.67693.5
2.64-2.6950.53984890.8720.2460.5960.70493.2
2.69-2.755.10.48784430.9020.2220.5380.70192.8
2.75-2.815.10.3884300.9270.1730.4210.73292.4
2.81-2.895.10.3684090.9340.1640.3980.75392.2
2.89-2.965.10.29483770.9510.1340.3250.78891.7
2.96-3.055.10.24483420.9640.110.270.84291.1
3.05-3.155.10.20583170.970.0930.2270.91491.2
3.15-3.265.10.17283670.9780.0780.191.0291.2
3.26-3.395.10.13983990.9850.0620.1531.16991.5
3.39-3.545.20.12183880.9870.0540.1331.26591.7
3.54-3.735.20.10185470.9910.0450.1121.40192.9
3.73-3.965.30.08786810.9930.0390.0961.58894.4
3.96-4.265.50.07688540.9950.0330.0831.68495.9
4.26-4.695.80.06389970.9960.0270.0691.69997.4
4.69-5.356.40.05892250.9970.0240.0631.41999.1
5.35-6.76.80.05393150.9980.0210.0571.0799.5
6.7-206.70.03895180.9980.0150.0410.99898.9

-
Processing

Software
NameVersionClassification
CNSrefinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QNE

2qne


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2177 15657 8.5 %
Rwork0.1745 142180 -
obs-157837 85.5 %
Solvent computationBsol: 54.8941 Å2
Displacement parametersBiso max: 127.52 Å2 / Biso mean: 47.1297 Å2 / Biso min: 9.33 Å2
Baniso -1Baniso -2Baniso -3
1--5.671 Å20 Å20 Å2
2---5.671 Å20 Å2
3---11.343 Å2
Refinement stepCycle: final / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22636 0 72 574 23282
Biso mean--72.91 40.75 -
Num. residues----2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.256
X-RAY DIFFRACTIONc_mcbond_it3.661.5
X-RAY DIFFRACTIONc_scbond_it6.2482
X-RAY DIFFRACTIONc_mcangle_it4.9612
X-RAY DIFFRACTIONc_scangle_it7.7832.5
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 RworkNum. reflection all% reflection obs (%)
2.5-2.590.315412890.2713117871307671.7
2.59-2.690.309314400.2603131061454679.4
2.69-2.810.302314390.2357132521469180.1
2.81-2.960.290814810.2326133651484681.2
2.96-3.150.283315070.2215136781518582.6
3.15-3.390.252215680.2018140291559784.7
3.39-3.730.235716070.1911145931620087.8
3.73-4.260.193516780.1543152351691391.5
4.26-5.350.163618020.127162011800396.6
5.35-200.171318460.1371169341878098.6
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 DIFFRACTION7na6.param
X-RAY DIFFRACTION8gol.param
X-RAY DIFFRACTION9cis_peptide_40pro111thr223pro.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