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- PDB-6l08: Crystal structure of Arabidopsis cytidine deaminase -

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Basic information

Entry
Database: PDB / ID: 6l08
TitleCrystal structure of Arabidopsis cytidine deaminase
ComponentsCytidine deaminase 1
KeywordsMETAL BINDING PROTEIN / pyrimidine metabolism / RNA editing / catalytic mechanism
Function / homology
Function and homology information


cytidine catabolic process / cytidine deaminase / cytidine deamination / : / cytidine deaminase activity / protein homodimerization activity / mitochondrion / zinc ion binding / cytosol
Similarity search - Function
Cytidine deaminase, homodimeric / Cytidine/deoxycytidylate deaminase, zinc-binding domain / Cytidine and deoxycytidylate deaminase zinc-binding region / 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
Cytidine deaminase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.999 Å
AuthorsJia, W. / Xiao, W. / Lin, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of Arabidopsis thaliana cytidine deaminase.
Authors: Wang, J. / Guo, Q. / Liu, L. / Wang, X.
History
DepositionSep 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytidine deaminase 1
B: Cytidine deaminase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1643
Polymers67,0672
Non-polymers961
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-34 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.644, 112.644, 111.585
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cytidine deaminase 1 / At-CDA1


Mass: 33533.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CDA1, CDD, DESZ, At2g19570, F3P11 / Production host: Escherichia coli (E. coli) / References: UniProt: O65896, cytidine deaminase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion
Details: 0.1 M MES sodium salt pH6.5, 2.0 M ammonium sulfate, 5% (w/v) PEG 400 and 0.1 M TCEP hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 16815 / % possible obs: 99.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 54.93 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.022 / Rrim(I) all: 0.069 / Χ2: 0.937 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.1110.41.3816670.7990.451.4540.88999.9
3.11-3.2310.40.92816490.870.3020.9770.906100
3.23-3.3810.20.55916620.9470.1840.5890.893100
3.38-3.5610.10.33316460.9820.110.3510.90999.9
3.56-3.789.90.18516840.9940.0620.1960.95599.9
3.78-4.079.40.10916650.9970.0370.1160.95499.5
4.07-4.489.20.06116670.9980.0210.0650.99198.9
4.48-5.1310.30.04317000.9990.0140.0451.061100
5.13-6.469.90.03717010.9990.0120.0390.97599.8
6.46-508.50.02417740.9990.0080.0250.82598.7

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AF2

1af2


Resolution: 2.999→39.637 Å / FOM work R set: 0.7774 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2846 683 5 %
Rwork0.2491 12987 -
obs0.2508 13670 81.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 350.6 Å2 / Biso mean: 99.65 Å2 / Biso min: 27.85 Å2
Refinement stepCycle: final / Resolution: 2.999→39.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 5 43 4163
Biso mean--92.46 70.04 -
Num. residues----569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034232
X-RAY DIFFRACTIONf_angle_d0.8385789
X-RAY DIFFRACTIONf_chiral_restr0.057670
X-RAY DIFFRACTIONf_plane_restr0.004774
X-RAY DIFFRACTIONf_dihedral_angle_d11.081463
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9995-3.2310.3245720.3059121039
3.231-3.55590.32811330.2823229573
3.5559-4.070.29991540.2573300095
4.07-5.12610.24041650.2304318399
5.1261-39.6370.28931590.2392329999
Refinement TLS params.Method: refined / Origin x: 18.9432 Å / Origin y: -28.5695 Å / Origin z: 14.8816 Å
111213212223313233
T1.0548 Å2-0.1384 Å20.0668 Å2-0.4492 Å2-0.2958 Å2--0.5177 Å2
L2.7755 °20.5806 °2-0.9492 °2-2.1398 °2-1.2871 °2--2.6326 °2
S-0.6115 Å °0.8796 Å °-0.5103 Å °-1.2029 Å °0.2436 Å °-0.2402 Å °1.0816 Å °-0.3403 Å °0.1004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 301
2X-RAY DIFFRACTION1allA400 - 1043
3X-RAY DIFFRACTION1allB0 - 300
4X-RAY DIFFRACTION1allB1000 - 1044

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