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- PDB-7zob: Metagenomic cytidine deaminase Cdd -

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Basic information

Entry
Database: PDB / ID: 7zob
TitleMetagenomic cytidine deaminase Cdd
ComponentsMetagenomic cytidine deaminase Cdd
KeywordsHYDROLASE
Function / homologyCytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsTamulaitiene, G. / Urbeliene, N. / Meskys, R.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Other government01.2.2-LMT-K-718-03-0082Lithuania
CitationJournal: Sci Adv / Year: 2023
Title: Cytidine deaminases catalyze the conversion of N ( S , O ) 4 -substituted pyrimidine nucleosides.
Authors: Urbeliene, N. / Tiskus, M. / Tamulaitiene, G. / Gasparaviciute, R. / Lapinskaite, R. / Jauniskis, V. / Sudzius, J. / Meskiene, R. / Tauraite, D. / Skrodenyte, E. / Urbelis, G. / Vaitekunas, J. / Meskys, R.
History
DepositionApr 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metagenomic cytidine deaminase Cdd
B: Metagenomic cytidine deaminase Cdd
C: Metagenomic cytidine deaminase Cdd
D: Metagenomic cytidine deaminase Cdd
E: Metagenomic cytidine deaminase Cdd
F: Metagenomic cytidine deaminase Cdd
G: Metagenomic cytidine deaminase Cdd
H: Metagenomic cytidine deaminase Cdd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,67234
Polymers123,0668
Non-polymers2,60626
Water12,863714
1
A: Metagenomic cytidine deaminase Cdd
B: Metagenomic cytidine deaminase Cdd
C: Metagenomic cytidine deaminase Cdd
D: Metagenomic cytidine deaminase Cdd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,74016
Polymers61,5334
Non-polymers1,20712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15020 Å2
ΔGint-355 kcal/mol
Surface area17350 Å2
2
E: Metagenomic cytidine deaminase Cdd
F: Metagenomic cytidine deaminase Cdd
hetero molecules

E: Metagenomic cytidine deaminase Cdd
F: Metagenomic cytidine deaminase Cdd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,12420
Polymers61,5334
Non-polymers1,59116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area15280 Å2
ΔGint-364 kcal/mol
Surface area17650 Å2
3
G: Metagenomic cytidine deaminase Cdd
H: Metagenomic cytidine deaminase Cdd
hetero molecules

G: Metagenomic cytidine deaminase Cdd
H: Metagenomic cytidine deaminase Cdd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,74016
Polymers61,5334
Non-polymers1,20712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area15080 Å2
ΔGint-345 kcal/mol
Surface area17430 Å2
Unit cell
Length a, b, c (Å)97.484, 128.899, 97.259
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-306-

HOH

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Components

#1: Protein
Metagenomic cytidine deaminase Cdd


Mass: 15383.194 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: cdd / Plasmid: pLATE3 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 28% 2-methyl-2,4-pentanediol, 0.02 M magnesium acetate, 0.1 M Na-MES, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→77.752 Å / Num. all: 371946 / Num. obs: 371946 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 12.97 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.076 / Rsym value: 0.057 / Net I/av σ(I): 4.8 / Net I/σ(I): 18.8 / Num. measured all: 2430277
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.2-1.266.60.3052.2357179541190.140.3660.3057.199.4
1.26-1.346.40.2113.2327759512570.1010.2590.2119.199.8
1.34-1.436.30.1474.6302875483800.0730.1860.14711.6100
1.43-1.556.60.0927.3298139449830.0460.120.09216.5100
1.55-1.76.60.0659.8273892414190.0340.090.06521.5100
1.7-1.96.40.05211.7239133374550.0290.0730.05225.599.9
1.9-2.1970.04712.6232725331060.0230.0620.04730.999.9
2.19-2.6870.04513.2194810279520.0210.0570.04532.999.9
2.68-3.796.30.05110135204215150.0280.0680.05132.299.5
3.79-77.7525.80.0639.468561117600.0370.0860.0633198.2

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Processing

Software
NameVersionClassification
PHENIXphenix-1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
XDSVERSION Feb 5, 2021data reduction
SCALA6.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model using 1jtk as a template

1jtk


Resolution: 1.2→60.72 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.69 / Phase error: 13.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1614 72696 9.92 %
Rwork0.1455 660091 -
obs0.1471 371871 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.54 Å2 / Biso mean: 18.0733 Å2 / Biso min: 9.05 Å2
Refinement stepCycle: final / Resolution: 1.2→60.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8073 0 146 714 8933
Biso mean--13.49 26.37 -
Num. residues----1075
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.210.19524810.1745217762425798
1.21-1.230.187124570.1606220592451699
1.23-1.240.17524260.1593219492437599
1.24-1.260.169324120.1557220412445399
1.26-1.280.165323730.1497220702444399
1.28-1.290.164123410.1449221962453799
1.29-1.310.167124430.1456221242456799
1.31-1.330.172223120.1524221022441499
1.33-1.350.167623860.1504221172450399
1.35-1.370.157224530.1467220522450599
1.37-1.40.159525020.1385219762447899
1.4-1.420.141225270.1241220642459199
1.42-1.450.139824570.1212221512460899
1.45-1.480.140924610.1216219272438899
1.48-1.510.137324930.1164219362442999
1.51-1.550.133624350.1117222572469299
1.55-1.590.140823790.1175220132439299
1.59-1.630.140423930.1218219632435699
1.63-1.680.144624250.1234220692449499
1.68-1.730.141325180.1222219542447299
1.73-1.790.142723520.1251220102436299
1.79-1.860.142424370.1283220522448999
1.86-1.950.158724290.1335221622459199
1.95-2.050.148124360.13522206124497100
2.05-2.180.140525020.13122218124683100
2.18-2.350.152624250.13262206724492100
2.35-2.590.157223560.14122225724613100
2.59-2.960.172422970.1555222292452699
2.96-3.730.164924140.1529215482396297
3.73-60.720.202923740.1939207282310293

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