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- PDB-7fh4: Chlorovirus PBCV-1 bi-functional dCMP/dCTP deaminase bi-DCD -

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Basic information

Entry
Database: PDB / ID: 7fh4
TitleChlorovirus PBCV-1 bi-functional dCMP/dCTP deaminase bi-DCD
ComponentsCMP/dCMP-type deaminase domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / deaminase / bi-function / dCMP / dCTP
Function / homology
Function and homology information


dCMP deaminase activity / pyrimidine nucleotide metabolic process / zinc ion binding
Similarity search - Function
Deoxycytidylate deaminase domain / Deoxycytidylate deaminase-related / Deoxycytidylate deaminase / 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
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / CMP/dCMP-type deaminase domain-containing protein
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.996 Å
AuthorsShe, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0504900 China
CitationJournal: Arch.Biochem.Biophys. / Year: 2022
Title: Structural basis of a multi-functional deaminase in chlorovirus PBCV-1.
Authors: Li, Y.H. / Hou, H.F. / Geng, Z. / Zhang, H. / She, Z. / Dong, Y.H.
History
DepositionJul 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: 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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CMP/dCMP-type deaminase domain-containing protein
B: CMP/dCMP-type deaminase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,54610
Polymers31,8182
Non-polymers1,7288
Water2,414134
1
A: CMP/dCMP-type deaminase domain-containing protein
B: CMP/dCMP-type deaminase domain-containing protein
hetero molecules

A: CMP/dCMP-type deaminase domain-containing protein
B: CMP/dCMP-type deaminase domain-containing protein
hetero molecules

A: CMP/dCMP-type deaminase domain-containing protein
B: CMP/dCMP-type deaminase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,63930
Polymers95,4556
Non-polymers5,18424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area23280 Å2
ΔGint-80 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.582, 81.582, 80.396
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CMP/dCMP-type deaminase domain-containing protein / bi-DCD protein


Mass: 15909.087 Da / Num. of mol.: 2 / Mutation: E69Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Gene: A596R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O41078

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Non-polymers , 5 types, 142 molecules

#2: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1M sodium acetate PH 5.8, 4% PEG 4000, 12% MPD, 2.5mM MgCl2, 2.5mM dCTP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.2797 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2797 Å / Relative weight: 1
ReflectionResolution: 1.996→40.791 Å / Num. obs: 40426 / % possible obs: 99.7 % / Redundancy: 9.3 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.106 / Net I/σ(I): 10.1
Reflection shellResolution: 1.996→2.0199 Å / Num. unique obs: 1216 / CC1/2: 0.656

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.996→40.791 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 3886 9.61 %
Rwork0.1702 36540 -
obs0.1744 40426 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.82 Å2 / Biso mean: 43.4705 Å2 / Biso min: 23.64 Å2
Refinement stepCycle: final / Resolution: 1.996→40.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 100 134 2432
Biso mean--42.95 47.22 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072344
X-RAY DIFFRACTIONf_angle_d1.0943184
X-RAY DIFFRACTIONf_chiral_restr0.098344
X-RAY DIFFRACTIONf_plane_restr0.005394
X-RAY DIFFRACTIONf_dihedral_angle_d14.9961362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.996-2.01990.28251250.2825121691
2.0199-2.04550.32411440.3025130198
2.0455-2.07240.35681320.2972123897
2.0724-2.10080.34141400.2851128198
2.1008-2.13080.35321360.2582129098
2.1308-2.16260.29681310.2276133099
2.1626-2.19640.27891380.20951324100
2.1964-2.23240.29351460.20431270100
2.2324-2.27090.31391360.22211333100
2.2709-2.31220.26011420.20281296100
2.3122-2.35670.23341400.17991320100
2.3567-2.40480.26871420.17051329100
2.4048-2.45710.23141440.16091273100
2.4571-2.51420.23931420.16511335100
2.5142-2.57710.24921440.17431307100
2.5771-2.64670.2561380.16191307100
2.6467-2.72460.20321370.17291350100
2.7246-2.81250.29141400.18021300100
2.8125-2.9130.21931340.16921307100
2.913-3.02960.18051400.16331326100
3.0296-3.16750.19361360.17281308100
3.1675-3.33440.21911360.17451309100
3.3344-3.54320.20191440.18231345100
3.5432-3.81660.23571460.15271298100
3.8166-4.20030.17411420.13891297100
4.2003-4.80730.16981440.13231325100
4.8073-6.05350.17041390.15571306100
6.0535-40.7910.17021280.1644131999
Refinement TLS params.Method: refined / Origin x: 19.365 Å / Origin y: -22.1771 Å / Origin z: 17.4263 Å
111213212223313233
T0.247 Å20.0051 Å2-0.0051 Å2-0.3433 Å20.0218 Å2--0.3175 Å2
L0.7532 °2-0.0883 °20.1149 °2-1.6075 °2-0.0806 °2--0.8169 °2
S0.0305 Å °0.0409 Å °0.0172 Å °-0.0653 Å °-0.006 Å °0.4149 Å °0.0139 Å °-0.2336 Å °-0.0293 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 142
2X-RAY DIFFRACTION1allB3 - 142
3X-RAY DIFFRACTION1allC1 - 4
4X-RAY DIFFRACTION1allD1 - 4
5X-RAY DIFFRACTION1allS1 - 135

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