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- PDB-5c2o: Crystal structure of Streptococcus mutans Deoxycytidylate Deamina... -

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Basic information

Entry
Database: PDB / ID: 5c2o
TitleCrystal structure of Streptococcus mutans Deoxycytidylate Deaminase complexed with dTTP
ComponentsPutative deoxycytidylate deaminase
KeywordsHYDROLASE / dCMP deaminase / inhibitor / allosteric regulation / enzyme complex
Function / homology
Function and homology information


dCMP deaminase activity / pyrimidine nucleotide metabolic process / nucleotide binding / zinc ion binding / cytoplasm
Similarity search - Function
Deoxycytidylate deaminase domain / 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. ...Deoxycytidylate deaminase domain / 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
THYMIDINE-5'-TRIPHOSPHATE / Deoxycytidylate deaminase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsLi, Y.H. / Gao, Z.Q. / Hou, H.F. / Dong, Y.H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Mechanism of the allosteric regulation of Streptococcus mutans 2'-deoxycytidylate deaminase.
Authors: Li, Y. / Guo, Z. / Jin, L. / Wang, D. / Gao, Z. / Su, X. / Hou, H. / Dong, Y.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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: Putative deoxycytidylate deaminase
B: Putative deoxycytidylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,10310
Polymers40,8282
Non-polymers1,2758
Water1,820101
1
A: Putative deoxycytidylate deaminase
B: Putative deoxycytidylate deaminase
hetero molecules

A: Putative deoxycytidylate deaminase
B: Putative deoxycytidylate deaminase
hetero molecules

A: Putative deoxycytidylate deaminase
B: Putative deoxycytidylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,30930
Polymers122,4856
Non-polymers3,82424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area23740 Å2
ΔGint-374 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.455, 112.455, 112.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Putative deoxycytidylate deaminase


Mass: 20414.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: ATCC 700610 / UA159 / Gene: comEB, SMU_1849 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q8DSE5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS, I_PLUS/MINUS COLUMNS
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.2824 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 19994 / % possible obs: 100 % / Redundancy: 15.6 % / Net I/σ(I): 56.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→31.189 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.94 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS, I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2116 1051 5.26 %
Rwork0.1831 --
obs0.1846 19994 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→31.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 64 101 2413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082348
X-RAY DIFFRACTIONf_angle_d1.1633194
X-RAY DIFFRACTIONf_dihedral_angle_d18.126856
X-RAY DIFFRACTIONf_chiral_restr0.043358
X-RAY DIFFRACTIONf_plane_restr0.005404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3505-2.45740.26751130.22842333X-RAY DIFFRACTION100
2.4574-2.58690.2487930.22572371X-RAY DIFFRACTION100
2.5869-2.74890.27181600.21922338X-RAY DIFFRACTION100
2.7489-2.9610.26381250.23552359X-RAY DIFFRACTION100
2.961-3.25870.24491350.2232332X-RAY DIFFRACTION100
3.2587-3.72960.22921490.18762343X-RAY DIFFRACTION100
3.7296-4.69630.18211280.15482406X-RAY DIFFRACTION100
4.6963-31.19210.16691480.1492461X-RAY DIFFRACTION100

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