[English] 日本語
Yorodumi
- PDB-1ufq: Crystal structure of ligand-free human uridine-cytidine kinase 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ufq
TitleCrystal structure of ligand-free human uridine-cytidine kinase 2
ComponentsUridine-cytidine kinase 2
KeywordsTRANSFERASE / ALPHA/BETA MONONUCLEOTIDE-BINDING HOLD
Function / homology
Function and homology information


uridine/cytidine kinase / CTP salvage / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / cellular response to oxygen levels / feeding behavior / response to axon injury / ATP binding ...uridine/cytidine kinase / CTP salvage / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / cellular response to oxygen levels / feeding behavior / response to axon injury / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
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
Uridine-cytidine kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSuzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F.
Citation
Journal: STRUCTURE / Year: 2004
Title: Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase
Authors: Suzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Crystallization and preliminary X-ray analysis of human uridine-cytidine kinase 2
Authors: Suzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F.
History
DepositionJun 6, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uridine-cytidine kinase 2
B: Uridine-cytidine kinase 2
C: Uridine-cytidine kinase 2
D: Uridine-cytidine kinase 2


Theoretical massNumber of molelcules
Total (without water)113,0524
Polymers113,0524
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-32 kcal/mol
Surface area36820 Å2
MethodPISA
2
A: Uridine-cytidine kinase 2
B: Uridine-cytidine kinase 2
C: Uridine-cytidine kinase 2
D: Uridine-cytidine kinase 2

A: Uridine-cytidine kinase 2
B: Uridine-cytidine kinase 2
C: Uridine-cytidine kinase 2
D: Uridine-cytidine kinase 2


Theoretical massNumber of molelcules
Total (without water)226,1048
Polymers226,1048
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area12600 Å2
ΔGint-79 kcal/mol
Surface area72180 Å2
MethodPISA
3
A: Uridine-cytidine kinase 2
B: Uridine-cytidine kinase 2
C: Uridine-cytidine kinase 2
D: Uridine-cytidine kinase 2

A: Uridine-cytidine kinase 2
B: Uridine-cytidine kinase 2
C: Uridine-cytidine kinase 2
D: Uridine-cytidine kinase 2


Theoretical massNumber of molelcules
Total (without water)226,1048
Polymers226,1048
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area12930 Å2
ΔGint-78 kcal/mol
Surface area71850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.057, 94.262, 156.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Uridine-cytidine kinase 2 / URIDINE-CYTIDINE KINASE


Mass: 28262.994 Da / Num. of mol.: 4 / Fragment: residues 1-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9BZX2, uridine/cytidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.35 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: PEG400, PEG3350, glycerol, HEPES, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD / Detector: CCD / Date: May 27, 2002
RadiationMonochromator: rotated-inclined monochromator, vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→40.41 Å / Num. all: 38404 / Num. obs: 38404 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3910 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UDW

1udw


Resolution: 2.5→40.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 302132.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 3769 10 %RANDOM
Rwork0.236 ---
all0.242 37658 --
obs0.237 37658 85.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2919 Å2 / ksol: 0.344901 e/Å3
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---3.45 Å20 Å2
3---2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6503 0 0 130 6633
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 616 9.9 %
Rwork0.286 5576 -
obs-6192 86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
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