[English] 日本語
Yorodumi
- PDB-3kty: Crystal Structure of Probable Methyltransferase from Bordetella p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kty
TitleCrystal Structure of Probable Methyltransferase from Bordetella pertussis Tohama I
ComponentsProbable methyltransferase
KeywordsTRANSFERASE / alpha-beta-alpha sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Methyltransferase
Function / homology
Function and homology information


RNA methyltransferase activity / RNA processing / RNA binding / cytoplasm
Similarity search - Function
RNA methyltransferase TrmJ/LasT / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable methyltransferase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.302 Å
AuthorsKim, Y. / Tesar, C. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Probable Methyltransferase SpoU from Bordetella pertussis Tohama I
Authors: Kim, Y. / Tesar, C. / Keigher, L. / Joachimiak, A.
History
DepositionNov 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable methyltransferase
B: Probable methyltransferase
C: Probable methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3747
Polymers55,9973
Non-polymers3764
Water2,306128
1
A: Probable methyltransferase

A: Probable methyltransferase


Theoretical massNumber of molelcules
Total (without water)37,3322
Polymers37,3322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2820 Å2
ΔGint-4 kcal/mol
Surface area15260 Å2
MethodPISA
2
B: Probable methyltransferase
C: Probable methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7086
Polymers37,3322
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-30 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.480, 69.514, 174.802
Angle α, β, γ (deg.)90.00, 95.16, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Probable methyltransferase


Mass: 18665.768 Da / Num. of mol.: 3 / Fragment: target domain 1 - 170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama I / Gene: BP1901 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q7VXA3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH7.5, 25 % w/v Polyehtlyene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→43.52 Å / Num. all: 22535 / Num. obs: 22535 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 43.52 Å2 / Rsym value: 0.117 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1130 / Rsym value: 0.623 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.302→43.52 Å / SU ML: 0.36 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1151 5.12 %random
Rwork0.187 ---
all0.19 22502 --
obs0.19 22502 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.368 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.5154 Å20 Å2-4.0082 Å2
2---1.9174 Å20 Å2
3----8.5979 Å2
Refinement stepCycle: LAST / Resolution: 2.302→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3823 0 22 128 3973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133999
X-RAY DIFFRACTIONf_angle_d1.4095462
X-RAY DIFFRACTIONf_dihedral_angle_d19.6151454
X-RAY DIFFRACTIONf_chiral_restr0.081646
X-RAY DIFFRACTIONf_plane_restr0.008723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3015-2.40620.33891460.25182616276297
2.4062-2.53310.2941470.225826592806100
2.5331-2.69180.29781360.207926892825100
2.6918-2.89960.26691480.207426562804100
2.8996-3.19130.27471440.198126632807100
3.1913-3.65290.21421330.178326842817100
3.6529-4.60140.2081460.15512672281899
4.6014-43.53150.20661510.16482712286399
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.9393-0.73771.67833.5531-1.72973.9265-0.0296-0.22520.2053-0.0950.1310.0746-0.2515-0.3503-0.09450.0570.03350.02010.0843-0.04150.0926-10.402230.6409104.4493
23.0523-2.30271.71651.7568-1.08424.8968-0.1903-0.13230.00910.16110.23980.0442-0.5553-0.21320.00680.3317-0.0393-0.02490.16810.02010.2254
32.10870.517-1.16452.5232-1.00836.8858-0.07010.1261-0.1550.1021-0.3099-0.2415-0.33060.0330.35360.2126-0.0024-0.05220.20950.05050.2609
Refinement TLS groupSelection details: chain C

+
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