[English] 日本語
Yorodumi
- PDB-8vlm: Crystal structure of the yeast cytosine deaminase (yCD) E64V-M100... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vlm
TitleCrystal structure of the yeast cytosine deaminase (yCD) E64V-M100W heterodimer
Components(Cytosine deaminase) x 2
KeywordsANTIFUNGAL PROTEIN / cytosine deaminase / resistance / heterodimer
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 / 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
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsPicard, M.-E. / Grenier, G. / Despres, P.C. / Dube, A.K. / Landry, C.R. / Shi, R.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-06954 Canada
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)298169 Canada
CitationJournal: Science / Year: 2024
Title: Compensatory mutations potentiate constructive neutral evolution by gene duplication.
Authors: Despres, P.C. / Dube, A.K. / Picard, M.E. / Grenier, J. / Shi, R. / Landry, C.R.
History
DepositionJan 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 4, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytosine deaminase
B: Cytosine deaminase
C: Cytosine deaminase
D: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,76012
Polymers79,2504
Non-polymers5108
Water54030
1
A: Cytosine deaminase
B: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8806
Polymers39,6252
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cytosine deaminase
D: Cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8806
Polymers39,6252
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.809, 112.090, 116.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cytosine deaminase / yCD / Cytosine aminohydrolase / Fluorocytosine resistance protein 1


Mass: 19868.666 Da / Num. of mol.: 2 / Mutation: E64V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FCY1, YPR062W, YP9499.17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12178, cytosine deaminase
#2: Protein Cytosine deaminase / yCD / Cytosine aminohydrolase / Fluorocytosine resistance protein 1


Mass: 19756.398 Da / Num. of mol.: 2 / Mutation: M100W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FCY1, YPR062W, YP9499.17 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q12178, cytosine deaminase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7
Details: 0.1 M HEPES pH 7, 10%(w/v) PEG 4000, 10% (v/v) Isopropanol, cryoprotected by the reservoir solution supplemented with 15% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18049 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18049 Å / Relative weight: 1
ReflectionResolution: 2.67→49.6 Å / Num. obs: 21119 / % possible obs: 100 % / Redundancy: 4.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.064 / Rrim(I) all: 0.145 / Χ2: 0.97 / Net I/σ(I): 7.6 / Num. measured all: 103453
Reflection shellResolution: 2.67→2.8 Å / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.755 / Num. measured all: 13570 / Num. unique obs: 2753 / CC1/2: 0.7 / Rpim(I) all: 0.369 / Rrim(I) all: 0.843 / Χ2: 0.82 / Net I/σ(I) obs: 2

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→45.36 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 1098 5.22 %RANDOM
Rwork0.1926 ---
obs0.1952 21047 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 20 30 4756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044802
X-RAY DIFFRACTIONf_angle_d0.6156443
X-RAY DIFFRACTIONf_dihedral_angle_d6.293657
X-RAY DIFFRACTIONf_chiral_restr0.045678
X-RAY DIFFRACTIONf_plane_restr0.004839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.790.28551180.25652462X-RAY DIFFRACTION100
2.79-2.940.30111110.24822461X-RAY DIFFRACTION100
2.94-3.120.35951420.24832459X-RAY DIFFRACTION100
3.12-3.360.30641350.22342464X-RAY DIFFRACTION100
3.36-3.70.28331380.19622475X-RAY DIFFRACTION100
3.7-4.240.24721500.18742488X-RAY DIFFRACTION100
4.24-5.340.19551520.1612505X-RAY DIFFRACTION100
5.34-45.360.1831520.16942635X-RAY DIFFRACTION100

+
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