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- PDB-4p9c: Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in... -

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Basic information

Entry
Database: PDB / ID: 4p9c
TitleCrystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dCMP and dUMP
ComponentsDeoxycytidylate deaminase
KeywordsHYDROLASE / dCMP deaminase / cytidine deaminase / deoxycytidylate deaminase / S-TIM5
Function / homology
Function and homology information


dCMP deaminase activity / pyrimidine nucleotide metabolic process / nucleotide binding / zinc ion binding / cytoplasm
Similarity search - Function
Deoxycytidylate deaminase-related / Deoxycytidylate deaminase / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 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 ...Deoxycytidylate deaminase-related / Deoxycytidylate deaminase / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / 2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Deoxycytidylate deaminase
Similarity search - Component
Biological speciesCyanophage S-TIM5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsMarx, A. / Alian, A.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The First Crystal Structure of a dTTP-bound Deoxycytidylate Deaminase Validates and Details the Allosteric-Inhibitor Binding Site.
Authors: Marx, A. / Alian, A.
History
DepositionApr 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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: Deoxycytidylate deaminase
B: Deoxycytidylate deaminase
C: Deoxycytidylate deaminase
D: Deoxycytidylate deaminase
E: Deoxycytidylate deaminase
F: Deoxycytidylate deaminase
G: Deoxycytidylate deaminase
H: Deoxycytidylate deaminase
I: Deoxycytidylate deaminase
J: Deoxycytidylate deaminase
K: Deoxycytidylate deaminase
L: Deoxycytidylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,46648
Polymers182,29712
Non-polymers8,16936
Water5,873326
1
A: Deoxycytidylate deaminase
E: Deoxycytidylate deaminase
F: Deoxycytidylate deaminase
J: Deoxycytidylate deaminase
K: Deoxycytidylate deaminase
L: Deoxycytidylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,23324
Polymers91,1486
Non-polymers4,08518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15310 Å2
ΔGint-71 kcal/mol
Surface area31910 Å2
MethodPISA
2
B: Deoxycytidylate deaminase
C: Deoxycytidylate deaminase
D: Deoxycytidylate deaminase
G: Deoxycytidylate deaminase
H: Deoxycytidylate deaminase
I: Deoxycytidylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,23324
Polymers91,1486
Non-polymers4,08518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15460 Å2
ΔGint-71 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.050, 147.210, 100.470
Angle α, β, γ (deg.)90.00, 95.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Deoxycytidylate deaminase


Mass: 15191.383 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanophage S-TIM5 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: H6WFU3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Mass: 307.197 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H14N3O7P
#4: Chemical
ChemComp-DU / 2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 308.182 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H13N2O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M MMT buffer pH 8, 25% (w/v) PEG 1500, 5mM Magnesium chloride and 5mM dCTP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9322 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 2.6→99.99 Å
Reflection shellResolution: 2.6→2.67 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SCALAdata scaling
RefinementResolution: 2.6→99.99 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26783 3031 5.1 %RANDOM
Rwork0.23068 ---
obs0.23257 56969 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.493 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20.72 Å2
2---1.2 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.6→99.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12534 0 492 326 13352
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 239 -
Rwork0.313 4174 -
obs--99.98 %

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