[English] 日本語
Yorodumi
- PDB-4iwn: Crystal structure of a putative methyltransferase CmoA in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iwn
TitleCrystal structure of a putative methyltransferase CmoA in complex with a novel SAM derivative
ComponentstRNA (cmo5U34)-methyltransferase
KeywordsTRANSFERASE / putative tRNA modification enzyme / SCM-SAH
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / carboxyl- or carbamoyltransferase activity / tRNA wobble uridine modification / S-adenosyl-L-methionine binding / protein homodimerization activity / cytosol
Similarity search - Function
Carboxy-S-adenosyl-L-methionine synthase / Methyltransferase domain 25 / 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
Chem-GEK / Carboxy-S-adenosyl-L-methionine synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsAller, P. / Lobley, C.M. / Byrne, R.T. / Antson, A.A. / Waterman, D.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA.
Authors: Byrne, R.T. / Whelan, F. / Aller, P. / Bird, L.E. / Dowle, A. / Lobley, C.M. / Reddivari, Y. / Nettleship, J.E. / Owens, R.J. / Antson, A.A. / Waterman, D.G.
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Non-polymer description
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: tRNA (cmo5U34)-methyltransferase
B: tRNA (cmo5U34)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5866
Polymers51,4642
Non-polymers1,1214
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-46 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.120, 91.380, 70.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

-
Components

#1: Protein tRNA (cmo5U34)-methyltransferase / methyltransferase CmoA


Mass: 25732.246 Da / Num. of mol.: 2 / Fragment: UNP residues 19-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cmoA, yecO, b1870, JW1859 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 substr. MG1655
References: UniProt: P76290, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-GEK / (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate / CARBOXY-S-ADENOSYLMETHIONINE


Mass: 442.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H22N6O7S
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus crystallization screen (Molecular Dimensions) condition E8: 0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, 0.1 M ...Details: Morpheus crystallization screen (Molecular Dimensions) condition E8: 0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, 0.1 M MOPS/HEPES sodium, pH 7.5, 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% w/v MPD, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2011 / Details: CRL
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.73→55.89 Å / Num. all: 52750 / Num. obs: 52750 / % possible obs: 99.9 % / Redundancy: 5 % / Rsym value: 0.056 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.73-1.7850.6481.21927438560.648100
1.78-1.8250.5081.51873037270.50899.9
1.82-1.8850.38621835236620.386100
1.88-1.9350.2972.61787035630.297100
1.93-250.2263.41723834260.22699.9
2-2.0750.1674.71680533470.167100
2.07-2.1550.1395.61620432390.139100
2.15-2.2350.1126.91559531050.112100
2.23-2.3350.0958.11493029750.09599.9
2.33-2.4550.0819.41425328550.081100
2.45-2.584.90.06811.11339327130.068100
2.58-2.744.90.05613.11269825980.05699.9
2.74-2.934.80.04615.11175924300.04699.9
2.93-3.164.90.03916.81113422800.03999.8
3.16-3.464.90.03517.11018120840.03599.9
3.46-3.874.70.03216.5909119260.03299.9
3.87-4.4750.02820.8842116970.02899.9
4.47-5.474.90.02621.2711714590.026100
5.47-7.744.80.02523.4549911530.02599.8
7.74-55.894.40.02125.328916550.02197.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
XSCALEdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IM8

1im8


Resolution: 1.73→55.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.096 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 2687 5.1 %RANDOM
Rwork0.1957 50019 --
obs0.1975 52706 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.75 Å2 / Biso mean: 31.1035 Å2 / Biso min: 13.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---3.76 Å2-0 Å2
3---4.01 Å2
Refinement stepCycle: LAST / Resolution: 1.73→55.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 76 273 3909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193749
X-RAY DIFFRACTIONr_bond_other_d0.0010.023550
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9725083
X-RAY DIFFRACTIONr_angle_other_deg0.87238151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6424.078179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75415631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3651525
X-RAY DIFFRACTIONr_chiral_restr0.10.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024271
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02892
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 212 -
Rwork0.295 3640 -
all-3852 -
obs--99.97 %
Refinement TLS params.

T23: 0.0041 Å2 / 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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7881-0.27880.11152.3180.27180.63930.0265-0.0597-0.05650.0857-0.0430.22180.0463-0.00850.01650.0777-0.00580.0140.22470.022720.04392.413533.4807
22.334-0.2445-0.39931.84650.15691.33510.07350.45140.0905-0.47540.01250.35910.1315-0.1938-0.0860.37950.006-0.13860.48390.092520.6938-4.98854.0826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 247
2X-RAY DIFFRACTION2B20 - 244

+
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