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- PDB-7fh9: chlorovirus PBCV-1 bi-functional dCMP/dCTP deaminase bi-DCD with ... -

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Basic information

Entry
Database: PDB / ID: 7fh9
Titlechlorovirus PBCV-1 bi-functional dCMP/dCTP deaminase bi-DCD with dTTP/dTMP bound
ComponentsCMP/dCMP-type deaminase domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / deaminase / bi-function / dTTP / dTMP
Function / homology
Function and homology information


dCMP deaminase activity / pyrimidine nucleotide metabolic process / nucleotide binding / 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
THYMIDINE-5'-PHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / CMP/dCMP-type deaminase domain-containing protein
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8035
Polymers15,9091
Non-polymers8944
Water2,036113
1
A: CMP/dCMP-type deaminase domain-containing protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)100,81930
Polymers95,4556
Non-polymers5,36524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/21
crystal symmetry operation11_755-x+y+2,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area19700 Å2
ΔGint-62 kcal/mol
Surface area34020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.239, 87.239, 87.747
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

21A-381-

HOH

31A-387-

HOH

41A-407-

HOH

51A-409-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 15909.087 Da / Num. of mol.: 1 / 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, 117 molecules

#2: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH 7.2, 50% MPD, 2.5mM MgCl2, 2.5mM dTTP

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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: Jan 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2797 Å / Relative weight: 1
ReflectionResolution: 1.9→43.873 Å / Num. obs: 29462 / % possible obs: 99.9 % / Redundancy: 19.8 % / Rrim(I) all: 0.115 / Net I/σ(I): 19.5
Reflection shellResolution: 1.9→1.9307 Å / Num. unique obs: 1235 / CC1/2: 0.931 / Rpim(I) all: 0.159 / Rrim(I) all: 0.711

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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: 1.9→43.873 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 2946 10 %
Rwork0.1682 26516 -
obs0.1706 29462 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.75 Å2 / Biso mean: 26.2425 Å2 / Biso min: 11.22 Å2
Refinement stepCycle: final / Resolution: 1.9→43.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1099 0 52 113 1264
Biso mean--23.29 36.57 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071174
X-RAY DIFFRACTIONf_angle_d0.981596
X-RAY DIFFRACTIONf_chiral_restr0.063172
X-RAY DIFFRACTIONf_plane_restr0.005197
X-RAY DIFFRACTIONf_dihedral_angle_d15.96691
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.93070.25021330.1999123598
1.9307-1.96390.25541400.18331257100
1.9639-1.99970.19391430.17981277100
1.9997-2.03810.20351380.16151261100
2.0381-2.07970.1881420.15831267100
2.0797-2.12490.20721390.1611262100
2.1249-2.17440.20671370.16591259100
2.1744-2.22870.17211380.16011259100
2.2287-2.2890.1761390.15871282100
2.289-2.35640.2211410.16331255100
2.3564-2.43240.24541360.17561270100
2.4324-2.51930.18481400.16521268100
2.5193-2.62020.22591390.1731248100
2.6202-2.73940.18411420.17271267100
2.7394-2.88380.2141370.18431264100
2.8838-3.06450.18551440.16491248100
3.0645-3.3010.18941440.17241274100
3.301-3.63310.17961410.15561281100
3.6331-4.15840.14871440.14741255100
4.1584-5.23780.15971430.15771250100
5.2378-43.8730.2181460.20321277100
Refinement TLS params.Method: refined / Origin x: 101.7307 Å / Origin y: 70.6589 Å / Origin z: 19.4302 Å
111213212223313233
T0.1217 Å2-0.0046 Å20.0267 Å2-0.1347 Å2-0.0188 Å2--0.1573 Å2
L1.4226 °2-0.1652 °2-0.2771 °2-1.0889 °20.1491 °2--1.8444 °2
S0.0752 Å °0.11 Å °0.1348 Å °-0.0465 Å °-0.0352 Å °-0.0191 Å °-0.1556 Å °-0.0329 Å °-0.0384 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 142
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 126

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