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- PDB-6sqz: Mouse dCTPase in complex with dCMPNPP -

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Basic information

Entry
Database: PDB / ID: 6sqz
TitleMouse dCTPase in complex with dCMPNPP
ComponentsdCTP pyrophosphatase 1
KeywordsHYDROLASE / dCMPNPP complex
Function / homology
Function and homology information


dCTP catabolic process / pyrimidine deoxyribonucleotide binding / dCTP diphosphatase / dCTP diphosphatase activity / nucleoside triphosphate catabolic process / pyrophosphatase activity / nucleoside triphosphate diphosphatase activity / DNA protection / magnesium ion binding / 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
Chem-0KX / dCTP pyrophosphatase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _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)38,6118
Polymers37,5822
Non-polymers1,0306
Water2,756153
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)77,22316
Polymers75,1644
Non-polymers2,05912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_777-y+2,-x+2,-z+5/21
Buried area18290 Å2
ΔGint-203 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.997, 58.997, 142.650
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: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 22 - 130 / Label seq-ID: 22 - 130

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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17N4O12P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.0, 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→55 Å / Num. obs: 20663 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→2.05 Å / Rmerge(I) obs: 1.14 / Num. unique obs: 2015 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→54.52 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.429 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.136
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1123 5.4 %RANDOM
Rwork0.1866 ---
obs0.1883 19540 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.27 Å2 / Biso mean: 38.846 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 1.9→54.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 60 153 2012
Biso mean--41.62 45.26 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191961
X-RAY DIFFRACTIONr_bond_other_d0.0020.021758
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9982695
X-RAY DIFFRACTIONr_angle_other_deg1.00234084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1255234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.1352495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4771515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
Refine LS restraints NCS

Ens-ID: 1 / Number: 6890 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2D
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 70 -
Rwork0.297 1395 -
all-1465 -
obs--99.93 %
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)
10.9152-0.0336-0.01990.94650.16482.6593-0.043-0.06050.1542-0.1129-0.02680.0104-0.1895-0.06710.06980.06390.036-0.03220.0403-0.02540.100951.583269.772178.5303
20.82470.593-0.01271.19150.55993.54010.0721-0.0902-0.0282-0.09110.0802-0.18230.6041.1069-0.15230.22820.22740.00150.3952-0.02570.162170.489951.7157178.2692
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 150
2X-RAY DIFFRACTION2D22 - 150

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