[English] 日本語
Yorodumi
- PDB-3sm3: Crystal Structure of SAM-dependent methyltransferases Q8PUK2_METM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sm3
TitleCrystal Structure of SAM-dependent methyltransferases Q8PUK2_METMA from Methanosarcina mazei. Northeast Structural Genomics Consortium Target MaR262.
ComponentsSAM-dependent methyltransferases
KeywordsTRANSFERASE / NESG / Structural Genomics / PSI-biology / Protein Structure Initiative / Northeast Structural Genomics / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


methyltransferase activity / methylation / metal ion binding
Similarity search - Function
ubiE/COQ5 methyltransferase family signature 2. / UbiE/COQ5 methyltransferase, conserved site / Methyltransferase type 11 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SAM-dependent methyltransferases
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.197 Å
AuthorsVorobiev, S. / Neely, H. / Seetharaman, J. / Snyder, A. / Patel, P. / Xiao, R. / Ciccosanti, C. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Snyder, A. / Patel, P. / Xiao, R. / Ciccosanti, C. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published / Year: 2009
Title: Crystal Structure of SAM-dependent methyltransferases Q8PUK2_METMA from Methanosarcina mazei.
Authors: Vorobiev, S. / Neely, H. / Seetharaman, J. / Snyder, A. / Patel, P. / Xiao, R. / Ciccosanti, C. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SAM-dependent methyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1584
Polymers26,9721
Non-polymers1863
Water1,69394
1
A: SAM-dependent methyltransferases
hetero molecules

A: SAM-dependent methyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3168
Polymers53,9432
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_756-x+2,y,-z+11
Buried area2900 Å2
ΔGint-52 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.589, 51.589, 207.028
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-301-

CA

Detailsdimer,63.21 kD,95.2%

-
Components

#1: Protein SAM-dependent methyltransferases


Mass: 26971.570 Da / Num. of mol.: 1 / Mutation: L51K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: ATCC BAA-159/DSM 3647/Goe1/Go1/JCM 11883/OCM 88 / Gene: MM_2332 / Plasmid: pET 21-23C, MaR262-RM.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q8PUK2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 7.5
Details: 27% PEG 400, 0.2 M calcium chloride, 5% glycerol, 0.1 M HEPES, pH 7.5 , Microbatch crystallization under oil , temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 17, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.197→50 Å / Num. all: 54511 / Num. obs: 54511 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 37.61 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 20.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.38 / Num. unique all: 5461 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.197→29.817 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.834 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1367 5.03 %RANDOM
Rwork0.192 ---
obs0.195 27171 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.908 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 120.99 Å2 / Biso mean: 45.939 Å2 / Biso min: 17.01 Å2
Baniso -1Baniso -2Baniso -3
1-5.822 Å20 Å2-0 Å2
2--5.822 Å20 Å2
3----11.644 Å2
Refinement stepCycle: LAST / Resolution: 2.197→29.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 9 94 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081743
X-RAY DIFFRACTIONf_angle_d1.1512349
X-RAY DIFFRACTIONf_chiral_restr0.079259
X-RAY DIFFRACTIONf_plane_restr0.005301
X-RAY DIFFRACTIONf_dihedral_angle_d18.086637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.197-2.2760.2991410.24825832724
2.276-2.3670.2631470.24525712718
2.367-2.4750.3251330.23825672700
2.475-2.6050.2441630.2225922755
2.605-2.7680.2891230.225622685
2.768-2.9820.2741520.20225552707
2.982-3.2810.2671250.18626052730
3.281-3.7550.2591320.17225912723
3.755-4.7280.1981270.14925882715
4.728-29.820.2051240.19825902714
Refinement TLS params.Method: refined / Origin x: 42.7765 Å / Origin y: 13.3895 Å / Origin z: 86.2179 Å
111213212223313233
T0.1687 Å2-0.0025 Å20.0025 Å2-0.17 Å2-0.0108 Å2--0.1711 Å2
L0.6763 °2-0.5272 °2-0.0175 °2-1.5348 °2-0.2149 °2--0.6851 °2
S0.0053 Å °-0.0322 Å °0.0539 Å °0.0254 Å °0.0138 Å °0.0662 Å °-0.0646 Å °-0.0377 Å °-0 Å °
Refinement TLS groupSelection details: chain A

+
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