[English] 日本語
Yorodumi
- PDB-1wk4: Crystal structure of ttk003001606 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wk4
TitleCrystal structure of ttk003001606
Componentsttk003001606
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ttk003001606 / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable acetyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKaminishi, T. / Sakai, H. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of ttk003001606
Authors: Kaminishi, T. / Sakai, H. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: ttk003001606
B: ttk003001606
C: ttk003001606
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1436
Polymers58,5573
Non-polymers5863
Water2,054114
1
A: ttk003001606
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7142
Polymers19,5191
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ttk003001606
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7142
Polymers19,5191
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ttk003001606
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7142
Polymers19,5191
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.332, 78.332, 197.038
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsA monomer is probably the biological unit.

-
Components

#1: Protein ttk003001606


Mass: 19519.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJ05
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.2 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, sodium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.96500, 0.97897, 0.97933
DetectorDetector: CCD / Date: Apr 11, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9651
20.978971
30.979331
ReflectionResolution: 2.8→50 Å / Num. obs: 33433 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 16.8 % / Biso Wilson estimate: 73.2 Å2 / Rsym value: 0.097 / Net I/σ(I): 30.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 17.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1685 / Rsym value: 0.574 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→47.19 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 322005.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1621 5 %RANDOM
Rwork0.217 ---
obs0.217 32263 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.7011 Å2 / ksol: 0.369931 e/Å3
Displacement parametersBiso mean: 73.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.12 Å29.97 Å20 Å2
2--12.12 Å20 Å2
3----24.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4149 0 36 114 4299
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.421.5
X-RAY DIFFRACTIONc_mcangle_it8.162
X-RAY DIFFRACTIONc_scbond_it7.932
X-RAY DIFFRACTIONc_scangle_it10.762.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.433 273 5.5 %
Rwork0.399 4724 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3MES_CNS_PAR.TXT

+
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