[English] 日本語
Yorodumi
- PDB-9k1k: Yeast Cytosine Deaminase mutant-M100H -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k1k
TitleYeast Cytosine Deaminase mutant-M100H
ComponentsCytosine deaminase
KeywordsANTITUMOR PROTEIN / Cytosine deaminase
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: 1.439 Å
AuthorsYung, K.W.Y. / Zheng, J.L. / Chan, M.K.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)AoE/P-705/16 Hong Kong
CitationJournal: To Be Published
Title: An engineered yeast cytosine deaminase with improved catalytic activity and stability for macrophage-mediated enzyme/prodrug therapy
Authors: Zheng, J.L. / Zhou, J.H. / Yung, K.W.Y. / Lee, M.M. / Chan, M.K.
History
DepositionOct 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

-
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)35,3366
Polymers35,0742
Non-polymers2624
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-164 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.077, 79.077, 55.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 7 - 158 / Label seq-ID: 7 - 158

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

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


Mass: 17536.969 Da / Num. of mol.: 2 / Mutation: M100H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: FCY1, YPR062W, YP9499.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12178, cytosine deaminase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium cacodylate, 0.16M sodium acetate, 24% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.439→50 Å / Num. obs: 62709 / % possible obs: 99.8 % / Redundancy: 11.4 % / Rpim(I) all: 0.025 / Net I/σ(I): 31.3
Reflection shellResolution: 1.44→1.49 Å / Num. unique obs: 6120 / Rpim(I) all: 0.122 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.439→27.958 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.173 / SU ML: 0.022 / Cross valid method: FREE R-VALUE / ESU R: 0.052 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1442 3090 4.946 %
Rwork0.1272 59391 -
all0.128 --
obs-62481 99.743 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.027 Å2
Baniso -1Baniso -2Baniso -3
1-0.041 Å2-0 Å2-0 Å2
2--0.041 Å2-0 Å2
3----0.083 Å2
Refinement stepCycle: LAST / Resolution: 1.439→27.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 4 331 2705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162293
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.6633285
X-RAY DIFFRACTIONr_angle_other_deg0.4651.5895307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5735308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.906516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46710449
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.01610117
X-RAY DIFFRACTIONr_chiral_restr0.0720.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
X-RAY DIFFRACTIONr_nbd_refined0.2160.2495
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22095
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21208
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21185
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2200
X-RAY DIFFRACTIONr_metal_ion_refined0.1990.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2540.24
X-RAY DIFFRACTIONr_nbd_other0.1380.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.213
X-RAY DIFFRACTIONr_mcbond_it2.4941.3051223
X-RAY DIFFRACTIONr_mcbond_other2.4891.3051223
X-RAY DIFFRACTIONr_mcangle_it3.7382.3471528
X-RAY DIFFRACTIONr_mcangle_other3.7382.3481529
X-RAY DIFFRACTIONr_scbond_it4.2421.5981220
X-RAY DIFFRACTIONr_scbond_other4.2091.5951219
X-RAY DIFFRACTIONr_scangle_it6.3922.8151755
X-RAY DIFFRACTIONr_scangle_other6.392.8161756
X-RAY DIFFRACTIONr_lrange_it10.3314.6552880
X-RAY DIFFRACTIONr_lrange_other9.04813.5382791
X-RAY DIFFRACTIONr_rigid_bond_restr2.4834736
X-RAY DIFFRACTIONr_ncsr_local_group_10.0730.054960
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.072940.05009
12AX-RAY DIFFRACTIONLocal ncs0.072940.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.439-1.4760.1272120.10142190.10345640.990.99497.08590.085
1.476-1.5160.1182530.08542980.08745520.9920.99699.9780.075
1.516-1.560.1132420.08140950.08343380.9920.99699.97690.073
1.56-1.6080.1172000.0840410.08242420.9920.99699.97640.074
1.608-1.6610.1081990.07838700.07940690.9920.9961000.073
1.661-1.7190.1051640.08538280.08639920.9930.9961000.082
1.719-1.7830.1211830.09436520.09538350.990.9951000.093
1.783-1.8560.1392010.10134890.10336910.9880.99499.97290.102
1.856-1.9380.1531760.11234200.11335960.9870.9921000.117
1.938-2.0320.1481540.1231990.12233530.9870.9921000.128
2.032-2.1410.1391740.12330520.12432260.9890.9911000.133
2.141-2.2710.1461650.12129040.12230690.9880.9911000.136
2.271-2.4260.1541230.12327510.12428740.9860.9911000.143
2.426-2.6190.141320.13425790.13427110.9870.991000.157
2.619-2.8660.1541170.14723460.14824630.9830.9871000.178
2.866-3.20.1591320.15621140.15622460.9850.9851000.186
3.2-3.6880.166990.15318990.15319990.9850.98799.950.188
3.688-4.4970.152750.14616020.14616770.9860.9871000.19
4.497-6.2790.156650.17112790.1713440.990.9871000.225
6.279-27.9580.211240.1857540.1857910.9740.97798.35650.265

+
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