[English] 日本語
Yorodumi
- PDB-3w34: Ternary complex of Thermus thermophilus HB8 uridine-cytidine kina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w34
TitleTernary complex of Thermus thermophilus HB8 uridine-cytidine kinase with substrates
ComponentsUridine kinase
KeywordsTRANSFERASE / kinase / nucleoside
Function / homology
Function and homology information


uridine/cytidine kinase / CTP salvage / uridine kinase activity / cytidine kinase activity / UMP salvage / ATP binding / cytoplasm
Similarity search - Function
Uridine kinase / Uridine kinase-like / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / Uridine kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsTomoike, F. / Nakagawa, N. / Masui, R. / Kuramitsu, S.
CitationJournal: Protein J. / Year: 2015
Title: Structural and Biochemical Studies on the Reaction Mechanism of Uridine-Cytidine Kinase
Authors: Tomoike, F. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionDec 10, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uridine kinase
B: Uridine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9166
Polymers47,4192
Non-polymers1,4974
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-10 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.730, 126.952, 61.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Uridine kinase / Cytidine monophosphokinase / Uridine monophosphokinase


Mass: 23709.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: udk, TTHA0578 / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q5SKR5, uridine/cytidine kinase
#2: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE


Mass: 243.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N3O5
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.84 Å3/Da / Density % sol: 56.68 % / Mosaicity: 0.772 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 50% of No 46 (0.1M sodium chloride, 0.1M BICINE, pH 9.0, 20% (v/v) polyethylene glycol monomethyl ether 550) from Crystal Screen 2 (Hampton Research), VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→24 Å / Num. obs: 42233 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.072 / Χ2: 1.447 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.91-1.936.70.52820740.9621100
1.93-1.976.70.43220820.8471100
1.97-2.016.70.36321030.8541100
2.01-2.056.70.31220950.874199.9
2.05-2.096.70.27320821.0021100
2.09-2.146.80.21421110.896199.7
2.14-2.196.70.18720850.95199.7
2.19-2.256.70.17220851.2721100
2.25-2.326.70.13820691.094199.5
2.32-2.396.70.12620951.094199.7
2.39-2.486.70.11321261.129199.5
2.48-2.586.80.09520811.212199.7
2.58-2.76.80.08621221.298199.5
2.7-2.846.80.07320821.363198.8
2.84-3.016.80.06721011.59198.9
3.01-3.256.80.06721122.119198.1
3.25-3.576.70.06421082.893198.3
3.57-4.096.60.0621403.323198.7
4.09-5.1470.04121742.313199.9
5.14-246.70.03123061.732199.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→24 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2434 4251 9.8 %
Rwork0.2093 37933 -
obs-42184 97.3 %
Solvent computationBsol: 27.7672 Å2
Displacement parametersBiso max: 140.03 Å2 / Biso mean: 27.4543 Å2 / Biso min: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.546 Å20 Å20 Å2
2---0.54 Å20 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.91→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 60 201 3529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.7861.5
X-RAY DIFFRACTIONc_scbond_it2.9962
X-RAY DIFFRACTIONc_mcangle_it2.4862
X-RAY DIFFRACTIONc_scangle_it4.3042.4
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 49

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.91-1.930.3307660.2395682748
1.93-1.940.3297960.2696746842
1.94-1.950.308880.2596767855
1.95-1.970.2876860.2519775861
1.97-1.980.3075760.255769845
1.98-20.3008860.2528763849
2-2.010.2764930.2261782875
2.01-2.030.2409790.2157743822
2.03-2.050.27321000.2248762862
2.05-2.060.2805810.2262783864
2.06-2.080.2898920.2282756848
2.08-2.10.2705870.2333763850
2.1-2.120.2476910.2031764855
2.12-2.140.2872970.2143758855
2.14-2.160.24841070.2166749856
2.16-2.180.2618890.2131761850
2.18-2.20.2187870.1855790877
2.2-2.230.2349900.205738828
2.23-2.250.2717910.2106771862
2.25-2.280.2604780.2217783861
2.28-2.30.2898680.2087792860
2.3-2.330.2193830.2062752835
2.33-2.360.2694910.1982791882
2.36-2.390.2454980.2123743841
2.39-2.430.2158850.2081773858
2.43-2.460.3003960.2307762858
2.46-2.50.2362700.2202798868
2.5-2.540.2419820.2067759841
2.54-2.580.2246750.2078806881
2.58-2.620.2153820.1951757839
2.62-2.670.2456990.2106775874
2.67-2.720.2695800.2252774854
2.72-2.780.2737800.2265775855
2.78-2.840.2214890.2129762851
2.84-2.90.2274800.2095781861
2.9-2.980.2827940.2298756850
2.98-3.060.25331030.2326746849
3.06-3.150.2528810.2228786867
3.15-3.250.2389990.2272761860
3.25-3.360.2603650.2198792857
3.36-3.50.2592870.2114755842
3.5-3.660.1986850.2024800885
3.66-3.850.2466850.1845787872
3.85-4.090.2561780.1874791869
4.09-4.40.1908790.1689818897
4.4-4.840.1924910.1685789880
4.84-5.530.224870.1982817904
5.53-6.940.2317910.2251832923
6.94-240.22571000.2081862962
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ctn.param
X-RAY DIFFRACTION4acp.param

+
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