[English] 日本語
Yorodumi
- PDB-1uaq: The crystal structure of yeast cytosine deaminase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uaq
TitleThe crystal structure of yeast cytosine deaminase
Componentscytosine deaminase
KeywordsHYDROLASE / alpha-beta-alpha
Function / homology
Function and homology information


cytidine metabolic process / pyrimidine-containing compound salvage / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / cytosine deaminase / cytosine deaminase activity / : / UMP salvage / cytosine metabolic process / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / Cytosine deaminase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsKo, T.-P. / Lin, J.-J. / Hu, C.-Y. / Hsu, Y.-H. / Wang, A.H.-J. / Liaw, S.-H.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution
Authors: Ko, T.-P. / Lin, J.-J. / Hu, C.-Y. / Hsu, Y.-H. / Wang, A.H.-J. / Liaw, S.-H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary crystallographic analysis of yeast cytosine deaminase
Authors: Hsu, Y.-H. / Hu, C.-Y. / Lin, J.-J. / Liaw, S.-H.
History
DepositionMar 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: cytosine deaminase
B: cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4196
Polymers35,0602
Non-polymers3594
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-85 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.113, 53.681, 68.076
Angle α, β, γ (deg.)90.00, 105.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein cytosine deaminase


Mass: 17530.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: fcy1 / Plasmid: pET-6H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: Q12178, cytosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DUC / DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / DIHYDROURACIL


Mass: 114.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.07 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: isopropanol, PEG4000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: Hsu, Y.-H., (2003) Acta Crystallogr., Sect.D, 59, 950.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %2-propanol1reservoir
220 %PEG40001reservoir
30.1 Msodium HEPES1reservoirpH7.5
430 mg/mlprotein1drop
50-20 mM2-hydroxypyrimidine1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2002
RadiationMonochromator: the rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 42187 / Num. obs: 42187 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.057 / Net I/σ(I): 11.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3945 / Rsym value: 0.297 / % possible all: 91.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 277542
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 91.2 % / Num. unique obs: 3945 / Num. measured obs: 18894 / Rmerge(I) obs: 0.338

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.6→23.79 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1095 -RANDOM
Rwork0.177 ---
all0.178 43400 --
obs0.177 38222 88.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.161 Å20 Å27.895 Å2
2--0.223 Å20 Å2
3----0.063 Å2
Refine analyzeLuzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 18 484 2858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 1.6→1.66 Å /
Num. reflection% reflection
Rfree1905 -
obs18894 91.2 %
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Rfactor Rfree: 0.313 / Rfactor Rwork: 0.268 / Num. reflection obs: 3157

+
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