[English] 日本語
Yorodumi
- PDB-7cta: Crystal structure of Cx-SAM bound CmoB from Vibrio vulnificus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cta
TitleCrystal structure of Cx-SAM bound CmoB from Vibrio vulnificus
ComponentstRNA U34 carboxymethyltransferase
KeywordsTRANSFERASE / carboxymethyl transferase / tRNA modification / Cx-SAM
Function / homology
Function and homology information


tRNA wobble uridine modification / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / methyltransferase activity
Similarity search - Function
tRNA U34 carboxymethyltransferase / tRNA (Mo5U34)-methyltransferase-like / Protein of unknown function (DUF1698) / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-GEK / tRNA U34 carboxymethyltransferase / tRNA U34 carboxymethyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKim, J. / Jeong, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural snapshots of CmoB in various states during wobble uridine modification of tRNA.
Authors: Jeong, S. / Kim, J.
History
DepositionAug 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA U34 carboxymethyltransferase
B: tRNA U34 carboxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8656
Polymers76,7882
Non-polymers1,0774
Water1,56787
1
A: tRNA U34 carboxymethyltransferase
B: tRNA U34 carboxymethyltransferase
hetero molecules

A: tRNA U34 carboxymethyltransferase
B: tRNA U34 carboxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,72912
Polymers153,5754
Non-polymers2,1548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)181.962, 50.574, 104.410
Angle α, β, γ (deg.)90.000, 122.700, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 0 - 325 / Label seq-ID: 1 - 326

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein tRNA U34 carboxymethyltransferase


Mass: 38393.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus MO6-24/O (bacteria) / Strain: MO6-24/O
Gene: cmoB, CRN46_03385, CRN52_23395, D8T49_20765, D8T54_03695, JS86_05215
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A087JHK9, UniProt: Q8DAP0*PLUS, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 87 / 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: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Lithium sulfate monohydrate, TRIS hydrochloride pH 8.5, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17780 / % possible obs: 97.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.075 / Rrim(I) all: 0.148 / Χ2: 0.607 / Net I/σ(I): 3.6 / Num. measured all: 65694
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.953.40.3668510.8890.2240.4310.45494
2.95-33.50.3798540.8960.2270.4430.51196.3
3-3.063.60.3518750.880.2110.4110.54196.5
3.06-3.123.70.3388720.9140.20.3950.51997.4
3.12-3.193.70.2838690.9430.1680.3310.54197.6
3.19-3.273.70.2888920.9440.1690.3350.52198.6
3.27-3.353.70.238920.9440.1370.2690.5299
3.35-3.443.50.2178690.9550.1330.2560.60998
3.44-3.543.60.1968860.9630.1180.230.59797.4
3.54-3.653.90.1559070.9790.090.180.57999.8
3.65-3.783.80.1589000.980.0930.1840.72399.7
3.78-3.943.90.1338940.9790.0780.1550.71798.1
3.94-4.113.80.1048810.9910.0610.120.57398.2
4.11-4.333.80.0968870.9890.0560.1120.63398.1
4.33-4.63.50.0858910.9910.0520.10.62496.8
4.6-4.963.90.0799050.9930.0460.0920.59399.2
4.96-5.463.90.0868970.9920.050.10.60699.2
5.46-6.243.80.0889070.9910.0520.1030.55297.9
6.24-7.863.60.0729090.9920.0430.0850.6297.8
7.86-503.60.0639420.9930.0370.0731.06196.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qnx

4qnx


Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.51 / SU ML: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 889 5 %RANDOM
Rwork0.1785 ---
obs0.181 16820 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.78 Å2 / Biso mean: 32.002 Å2 / Biso min: 1.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å2-0 Å2-4.08 Å2
2--1.06 Å2-0 Å2
3---1.3 Å2
Refinement stepCycle: final / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 70 87 5480
Biso mean--46.45 18.63 -
Num. residues----656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135548
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175029
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6397557
X-RAY DIFFRACTIONr_angle_other_deg1.1921.57411661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6765654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61121.891312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81315908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8441540
X-RAY DIFFRACTIONr_chiral_restr0.0630.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021189
Refine LS restraints NCS

Ens-ID: 1 / Number: 10618 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 59 -
Rwork0.274 1205 -
all-1264 -
obs--94.54 %

+
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