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- PDB-1vq2: CRYSTAL STRUCTURE OF T4-BACTERIOPHAGE DEOXYCYTIDYLATE DEAMINASE, ... -

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Basic information

Entry
Database: PDB / ID: 1vq2
TitleCRYSTAL STRUCTURE OF T4-BACTERIOPHAGE DEOXYCYTIDYLATE DEAMINASE, MUTANT R115E
ComponentsDEOXYCYTIDYLATE DEAMINASE
KeywordsHYDROLASE
Function / homology
Function and homology information


dCMP deaminase / dCMP deaminase activity / nucleotide biosynthetic process / pyrimidine nucleotide metabolic process / zinc ion binding
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
3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Deoxycytidylate deaminase
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsAlmog, R. / Maley, F. / Maley, G.F. / Maccoll, R. / Van Roey, P.
CitationJournal: Biochemistry / Year: 2004
Title: Three-Dimensional Structure of the R115E Mutant of T4-Bacteriophage 2'-Deoxycytidylate Deaminase
Authors: Almog, R. / Maley, F. / Maley, G.F. / Maccoll, R. / Van Roey, P.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionDec 21, 2004ID: 1TEO
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEOXYCYTIDYLATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6384
Polymers21,1971
Non-polymers4413
Water84747
1
A: DEOXYCYTIDYLATE DEAMINASE
hetero molecules

A: DEOXYCYTIDYLATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2768
Polymers42,3942
Non-polymers8826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area3870 Å2
ΔGint-113 kcal/mol
Surface area15530 Å2
MethodPISA
2
A: DEOXYCYTIDYLATE DEAMINASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)129,82824
Polymers127,1826
Non-polymers2,64618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area19760 Å2
ΔGint-375 kcal/mol
Surface area38450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.528, 114.528, 76.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein DEOXYCYTIDYLATE DEAMINASE / DCMP DEAMINASE


Mass: 21197.041 Da / Num. of mol.: 1 / Mutation: R115E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: CD / Production host: Escherichia coli (E. coli) / References: UniProt: P16006, dCMP deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DDN / 3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / ((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE


Type: DNA linking / Mass: 310.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.44 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, DTT, sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.286, 1.2809, 1.000
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: May 10, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2861
21.28091
311
ReflectionResolution: 2.2→50 Å / Num. obs: 15589 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.044
Reflection shellResolution: 2.2→2.3 Å / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→49.59 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2149024.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1516 9.8 %RANDOM
Rwork0.218 ---
obs0.218 15537 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.97 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å23.68 Å20 Å2
2---0.7 Å20 Å2
3---1.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 22 47 1389
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.771.5
X-RAY DIFFRACTIONc_mcangle_it1.332
X-RAY DIFFRACTIONc_scbond_it1.22
X-RAY DIFFRACTIONc_scangle_it1.882.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 261 10.3 %
Rwork0.276 2266 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PDP_DHZ_OH.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMPDP_DHZ_OH.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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