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- PDB-2hvv: Crystal structure of dCMP deaminase from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 2hvv
TitleCrystal structure of dCMP deaminase from Streptococcus mutans
Componentsdeoxycytidylate deaminase
KeywordsHYDROLASE / 3-layer (alpha-beta)-sandwich
Function / homology
Function and homology information


dCMP deaminase activity / pyrimidine nucleotide metabolic process / nucleotide binding / 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
Deoxycytidylate deaminase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsHou, H.F. / Gao, Z.Q. / Li, L.F. / Liang, Y.H. / Su, X.D. / Dong, Y.H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of Streptococcus mutans 2'-deoxycytidylate deaminase and its complex with substrate analog and allosteric regulator dCTP x Mg2+.
Authors: Hou, H.F. / Liang, Y.H. / Li, L.F. / Su, X.D. / Dong, Y.H.
History
DepositionJul 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,85814
Polymers40,8282
Non-polymers1,03012
Water61334
1
A: deoxycytidylate deaminase
B: deoxycytidylate deaminase
hetero molecules

A: deoxycytidylate deaminase
B: deoxycytidylate deaminase
hetero molecules

A: deoxycytidylate deaminase
B: deoxycytidylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,57542
Polymers122,4856
Non-polymers3,09036
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area21910 Å2
ΔGint-635 kcal/mol
Surface area32880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.233, 113.233, 113.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

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Components

#1: Protein deoxycytidylate deaminase


Mass: 20414.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: comEB / Plasmid: PET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DSE5, dCMP deaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.6 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-Cl, PH8.5, 15% glycerol, 1.5M Ammonium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.2829, 1.2835, 1.2000
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2005
RadiationMonochromator: Si(111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28291
21.28351
31.21
Reflection

D res high: 3 Å / D res low: 50 Å / % possible obs: 100

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs
13.517.61343790.1211.089975
13.527.51344130.1171.19975
12.436.41233960.1411.019961
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465010010.0511.15612.7
5.136.4610010.0831.15713.4
4.485.1310010.0751.15313.5
4.074.4810010.0871.02613.6
3.784.0710010.1161.04913.6
3.563.7810010.171.04213.6
3.383.5610010.2130.95913.6
3.233.3810010.3410.99613.6
3.113.2310010.5221.26913.6
33.1110010.7980.96613.6
6.465010020.0461.85612.7
5.136.4610020.0771.3413.4
4.485.1310020.071.11813.5
4.074.4810020.0871.06713.6
3.784.0710020.1151.03413.6
3.563.7810020.1660.96913.6
3.383.5610020.2150.9313.6
3.233.3810020.3350.91513.6
3.113.2310020.5060.87613.6
33.1110020.7930.8813.6
6.465010030.0471.08811.7
5.136.4610030.0821.05112.3
4.485.1310030.0831.06412.4
4.074.4810030.0991.0212.5
3.784.0710030.1280.94512.6
3.563.7810030.1950.95712.5
3.383.5610030.2811.11412.5
3.233.3810030.3950.98412.5
3.113.2310030.5880.94512.5
33.1110030.8820.97312.5
ReflectionResolution: 3→50 Å / Num. all: 9958 / Num. obs: 9958 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.7 % / Rmerge(I) obs: 0.108 / Χ2: 1.047 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.681 / Num. unique all: 972 / Χ2: 0.757 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength11.28294.77-6.95
13 wavelength21.24.1-2.48
13 wavelength31.28354.49-8.92
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Zn53.9920.3440.9180.2550.915
2Zn58.8110.20.8480.0660.982
3Zn600.1190.6150.1871.038
4Zn52.5230.1540.8580.180.939
Phasing dmFOM : 0.82 / FOM acentric: 0.83 / FOM centric: 0.78 / Reflection: 6263 / Reflection acentric: 5507 / Reflection centric: 756
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10-46.2260.940.950.9229820791
6.3-100.910.920.86863709154
5-6.30.870.890.781044915129
4.4-50.880.880.821055945110
3.8-4.40.80.810.7118601683177
3.5-3.80.680.690.611143104895

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 983 9.9 %RANDOM
Rwork0.223 ---
all0.229 9958 --
obs0.226 9574 96.7 %-
Solvent computationBsol: 51.908 Å2
Displacement parametersBiso mean: 48.976 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 44 34 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0075661.5
X-RAY DIFFRACTIONc_angle_deg1.480942
X-RAY DIFFRACTIONc_mcangle_it1.9442
X-RAY DIFFRACTIONc_scangle_it2.1752.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4SO4.param

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