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

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Basic information

Entry
Database: PDB / ID: 2hvw
TitleCrystal structure of dCMP deaminase from Streptococcus mutans
Componentsdeoxycytidylate deaminase
KeywordsHYDROLASE / 3-layer (alpha-beta)-sandwich / protein-liand 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / 3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / 1,4-DIETHYLENE DIOXIDE / Deoxycytidylate deaminase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 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: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 25, 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 / 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.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
C: deoxycytidylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,30421
Polymers61,2433
Non-polymers3,06218
Water14,124784
1
A: deoxycytidylate deaminase
B: deoxycytidylate deaminase
C: deoxycytidylate deaminase
hetero molecules

A: deoxycytidylate deaminase
B: deoxycytidylate deaminase
C: deoxycytidylate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,60942
Polymers122,4856
Non-polymers6,12336
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)95.498, 99.657, 141.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein deoxycytidylate deaminase


Mass: 20414.174 Da / Num. of mol.: 3
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

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Non-polymers , 6 types, 802 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: 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.: 3 / Source method: obtained synthetically / Formula: C9H15N2O8P
#6: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, PH6.5, 12% Dioxane, 1.6M Ammonium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 9.8 % / Av σ(I) over netI: 10.1 / Number: 726299 / Rmerge(I) obs: 0.066 / Χ2: 1 / D res high: 1.66 Å / D res low: 16 Å / Num. obs: 74017 / % possible obs: 92.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.561699.210.03719.7
2.833.5698.110.0441.05110
2.482.8397.210.0651.05610.1
2.252.4896.310.0821.05310.1
2.092.2595.410.1061.04310.1
1.972.0994.710.150.99210.1
1.871.9793.810.2140.97810.1
1.791.8793.210.3030.92910.1
1.721.7992.410.3950.90510
1.661.7268.610.4670.8857.2
ReflectionResolution: 1.66→16 Å / Num. all: 79673 / Num. obs: 74017 / % possible obs: 92.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.8 % / Rmerge(I) obs: 0.066 / Χ2: 0.996 / Net I/σ(I): 10.1
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.467 / Num. unique all: 5412 / Χ2: 0.885 / % possible all: 68.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.67 Å15.9 Å
Translation1.67 Å15.9 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HVV

2hvv


Resolution: 1.67→16 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.303 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. There were three positions for the depositor to locate two atoms (CG1/CG2) for the residues VAL(A32),VAL(A94),VAL(B32),VAL(B94) and VAL(C94) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. There were three positions for the depositor to locate two atoms (CG1/CG2) for the residues VAL(A32),VAL(A94),VAL(B32),VAL(B94) and VAL(C94) and (CD1/CD2) for LEU(C107). All these sites have almost the same electron density(about 4sigma), so he placed the alternate comformations with one of (CG1/CG2) or (CD1/CD2). There are chirality errors at CB center among those conformations.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 3722 5 %RANDOM
Rwork0.149 ---
all0.151 79673 --
obs0.15 74010 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.322 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.57 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.67→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 171 784 4475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223748
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9815087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5955436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70325.053188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.815645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6431521
X-RAY DIFFRACTIONr_chiral_restr0.1680.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022769
X-RAY DIFFRACTIONr_nbd_refined0.2080.22042
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22621
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2732
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.259
X-RAY DIFFRACTIONr_mcbond_it0.5721.52238
X-RAY DIFFRACTIONr_mcangle_it0.89223531
X-RAY DIFFRACTIONr_scbond_it1.46931694
X-RAY DIFFRACTIONr_scangle_it2.1384.51556
LS refinement shellResolution: 1.667→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 206 -
Rwork0.283 4161 -
obs-4367 76.53 %

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