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- PDB-5jfy: Crystal structure of a plant cytidine deaminase -

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Basic information

Entry
Database: PDB / ID: 5jfy
TitleCrystal structure of a plant cytidine deaminase
ComponentsDeoxycytidine deaminase
KeywordsHYDROLASE / Cytidine deaminase
Function / homology
Function and homology information


hydrolase activity / zinc ion binding
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
ACETATE ION / HEXANE-1,6-DIOL / Deoxycytidine deaminase
Similarity search - Component
Biological speciesBrassica oleracea var. capitata (cabbage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.101 Å
AuthorsTaylor, M.W. / Lee, J.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: To be published
Authors: Taylor, M.W. / Lee, J.E.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Data collection
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxycytidine deaminase
B: Deoxycytidine deaminase
C: Deoxycytidine deaminase
D: Deoxycytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,62821
Polymers59,4754
Non-polymers1,15217
Water3,585199
1
A: Deoxycytidine deaminase
B: Deoxycytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,23510
Polymers29,7382
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-108 kcal/mol
Surface area11410 Å2
MethodPISA
2
C: Deoxycytidine deaminase
D: Deoxycytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,39311
Polymers29,7382
Non-polymers6559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-112 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.808, 99.808, 143.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-204-

ACT

21B-204-

ACT

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Deoxycytidine deaminase /


Mass: 14868.873 Da / Num. of mol.: 4 / Fragment: UNP residues 19-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica oleracea var. capitata (cabbage)
Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: H2EMX8

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Non-polymers , 6 types, 216 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 58.93 % / Description: Bipyramidal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.0085 M CoCl2, 0.085 sodium acetate pH 4.6, 0.85 M 1,6-hexanediol, 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 20, 2015
Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→47.67 Å / Num. obs: 41687 / % possible obs: 97.9 % / Redundancy: 2.4 % / Biso Wilson estimate: 31.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7 / Num. measured all: 101431
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Net I/σ(I) obs% possible all
2.1-2.1620.607663932670.6221.495
8.91-47.672.50.0213385270.99938.984.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å44.64 Å
Translation2.1 Å44.64 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
Aimlessdata scaling
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3J
Resolution: 2.101→44.635 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 1952 4.67 %
Rwork0.1806 39866 -
obs0.1822 37797 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 262.41 Å2 / Biso mean: 51.2129 Å2 / Biso min: 18.33 Å2
Refinement stepCycle: final / Resolution: 2.101→44.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3533 0 122 199 3854
Biso mean--93.64 47.35 -
Num. residues----476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033659
X-RAY DIFFRACTIONf_angle_d0.54943
X-RAY DIFFRACTIONf_chiral_restr0.043558
X-RAY DIFFRACTIONf_plane_restr0.003645
X-RAY DIFFRACTIONf_dihedral_angle_d17.6071290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1005-2.1530.31961300.29642672280293
2.153-2.21120.30461400.27212866300699
2.2112-2.27630.28951390.25262822296199
2.2763-2.34980.26161390.23682833297299
2.3498-2.43380.24191400.22082882302299
2.4338-2.53120.26711400.20782851299199
2.5312-2.64640.24451390.198328743013100
2.6464-2.78590.20571390.186928783017100
2.7859-2.96040.191430.16762882302599
2.9604-3.18890.22041420.1642896303899
3.1889-3.50970.15541420.14992870301299
3.5097-4.01730.17181410.14232888302998
4.0173-5.06020.18441420.14372863300596
5.0602-44.64560.23531360.19532789292588

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