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- PDB-6sqw: Mouse dCTPase in complex with 5-Me-dCMP -

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Basic information

Entry
Database: PDB / ID: 6sqw
TitleMouse dCTPase in complex with 5-Me-dCMP
ComponentsdCTP pyrophosphatase 1
KeywordsHYDROLASE / 5-Me-dCMP complex
Function / homology
Function and homology information


dCTP catabolic process / dCTP diphosphatase / dCTP diphosphatase activity / pyrimidine deoxyribonucleotide binding / nucleoside triphosphate catabolic process / pyrophosphatase activity / nucleoside triphosphate diphosphatase activity / DNA protection / magnesium ion binding / nucleoplasm ...dCTP catabolic process / dCTP diphosphatase / dCTP diphosphatase activity / pyrimidine deoxyribonucleotide binding / nucleoside triphosphate catabolic process / pyrophosphatase activity / nucleoside triphosphate diphosphatase activity / DNA protection / magnesium ion binding / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
dCTP pyrophosphatase 1 / MazG-like family / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE / dCTP pyrophosphatase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsScaletti, E.R. / Claesson, M. / Helleday, H. / Jemth, A.S. / Stenmark, P.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: The First Structure of an Active Mammalian dCTPase and its Complexes With Substrate Analogs and Products.
Authors: Scaletti, E. / Claesson, M. / Helleday, T. / Jemth, A.S. / Stenmark, P.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 15, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dCTP pyrophosphatase 1
D: dCTP pyrophosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2736
Polymers37,5822
Non-polymers6914
Water3,207178
1
A: dCTP pyrophosphatase 1
D: dCTP pyrophosphatase 1
hetero molecules

A: dCTP pyrophosphatase 1
D: dCTP pyrophosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,54612
Polymers75,1644
Non-polymers1,3828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area19780 Å2
ΔGint-162 kcal/mol
Surface area19080 Å2
Unit cell
Length a, b, c (Å)58.516, 58.516, 140.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 21 - 131 / Label seq-ID: 21 - 131

Dom-IDAuth asym-IDLabel asym-ID
1AA
2DB

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Components

#1: Protein dCTP pyrophosphatase 1 / Deoxycytidine-triphosphatase 1 / dCTPase 1 / RS21-C6


Mass: 18790.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dctpp1, Tdrg-TL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QY93, dCTP diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-5CM / 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 321.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N3O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.75, 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.8→54.5 Å / Num. obs: 23533 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.2
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 32921 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→54.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.143 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.121
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 1253 5.3 %RANDOM
Rwork0.1917 ---
obs0.193 22280 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.04 Å2 / Biso mean: 35.905 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.8→54.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 44 178 2062
Biso mean--30.43 41.99 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191980
X-RAY DIFFRACTIONr_bond_other_d0.0020.021802
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9852709
X-RAY DIFFRACTIONr_angle_other_deg0.99334184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1985234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.29123.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78515317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8581518
X-RAY DIFFRACTIONr_chiral_restr0.0930.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02414
Refine LS restraints NCS

Ens-ID: 1 / Number: 7278 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2D
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 79 -
Rwork0.307 1616 -
all-1695 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.01450.3331-0.02981.26510.04041.8187-0.121-0.18610.2714-0.2394-0.11790.1747-0.262-0.10810.23880.09710.0603-0.09370.0598-0.07330.1485-7.197610.531635.5517
20.94280.681-0.16541.03850.48552.3691-0.0788-0.1747-0.1532-0.16520.0211-0.2570.23910.60960.05770.13770.11550.08070.22690.070.166911.7728-7.809234.8731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 150
2X-RAY DIFFRACTION2D21 - 150

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