[English] 日本語
Yorodumi
- PDB-2zpa: Crystal Structure of tRNA(Met) Cytidine Acetyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zpa
TitleCrystal Structure of tRNA(Met) Cytidine Acetyltransferase
ComponentsUncharacterized protein ypfI
KeywordsTRANSFERASE / RNA MODIFICATION ENZYME / RNA HELICASE / ACETYLTRANSFERASE / GCN5 ACETYLTRANSFERASE
Function / homology
Function and homology information


tRNAMet cytidine acetyltransferase / tRNA N-acetyltransferase activity / tRNA wobble cytosine modification / tRNA acetylation / tRNA binding / ATP binding / cytoplasm
Similarity search - Function
tRNA(Met) cytidine acetyltransferase, tail domain / Rossmann fold - #11040 / tRNA(Met) cytidine acetyltransferase TmcA / tRNA(Met) cytidine acetyltransferase TmcA, tRNA-binding domain / TmcA, C-terminal domain superfamily / tRNA-binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / Helicase ...tRNA(Met) cytidine acetyltransferase, tail domain / Rossmann fold - #11040 / tRNA(Met) cytidine acetyltransferase TmcA / tRNA(Met) cytidine acetyltransferase TmcA, tRNA-binding domain / TmcA, C-terminal domain superfamily / tRNA-binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / Helicase / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / ADENOSINE-5'-DIPHOSPHATE / tRNA(Met) cytidine acetyltransferase TmcA
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsChimnaronk, S. / Manita, T. / Yao, M. / Tanaka, I.
CitationJournal: Embo J. / Year: 2009
Title: RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon
Authors: Chimnaronk, S. / Suzuki, T. / Manita, T. / Ikeuchi, Y. / Yao, M. / Suzuki, T. / Tanaka, I.
History
DepositionJul 8, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein ypfI
B: Uncharacterized protein ypfI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,1396
Polymers150,9962
Non-polymers2,1424
Water6,305350
1
A: Uncharacterized protein ypfI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7353
Polymers75,4981
Non-polymers1,2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein ypfI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4043
Polymers75,4981
Non-polymers9062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.298, 100.990, 263.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Uncharacterized protein ypfI / tRNA(Met) cytidine acetyltransferase


Mass: 75498.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: TMCA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P76562, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% (w/v) PEG 5000 monomethyl ether, 50mM lithium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A10.9791,0.9797,0.9645
SYNCHROTRONPhoton Factory AR-NW12A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJan 30, 2006
ADSC QUANTUM 2102CCDFeb 28, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSMADMx-ray1
2MIRRORSSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97971
30.96451
411
ReflectionResolution: 2.35→50 Å / Num. all: 66310 / Num. obs: 66310 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 31.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6211 / Rsym value: 0.373 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.35→20 Å / Occupancy max: 1 / Occupancy min: 0.6 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 5079 7.4 %RANDOM
Rwork0.235 61032 --
all-66111 --
obs-66227 95.8 %-
Solvent computationBsol: 38.625 Å2
Displacement parametersBiso max: 100 Å2 / Biso mean: 47.45 Å2 / Biso min: 15.14 Å2
Baniso -1Baniso -2Baniso -3
1--3.115 Å20 Å20 Å2
2---4.562 Å20 Å2
3---7.676 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10407 0 134 350 10891
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0113
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9179
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.08
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.41
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3981.5
X-RAY DIFFRACTIONc_mcangle_it2.3632
X-RAY DIFFRACTIONc_scbond_it2.1512
X-RAY DIFFRACTIONc_scangle_it3.2652.5
LS refinement shellResolution: 2.35→2.43 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.342 471 0.0696 %
Rwork0.2907 5293 -
obs-5764 85.2 %

+
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