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- PDB-3tp1: Crystal Structure of the precatalytic M-PMV dUTPase - substrate (... -

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Basic information

Entry
Database: PDB / ID: 3tp1
TitleCrystal Structure of the precatalytic M-PMV dUTPase - substrate (dUPNPP) complex
ComponentsDEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE
KeywordsHYDROLASE / jelly roll
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral nucleocapsid / structural constituent of virion / aspartic-type endopeptidase activity / viral translational frameshifting / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / : / gag protein p24 N-terminal domain / Distorted Sandwich / Retropepsin-like catalytic domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Gag-Pro polyprotein / Gag-Pro polyprotein
Similarity search - Component
Biological speciesMason-pfizer monkey virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 1.6 Å
AuthorsBarabas, O. / Nemeth, V. / Vertessy, B.G.
Citation
Journal: To be Published
Title: Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion
Authors: Barabas, O. / Nemeth, V. / Bodor, A. / Perczel, A. / Rosta, E. / Kele, Z. / Zagyva, I. / Szabadka, Z. / Grolmusz, V.I. / Wilmanns, M. / Vertessy, B.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray studies of dUTPase from Mason-Pfizer monkey retrovirus.
Authors: Barabas, O. / Nemeth, V. / Vertessy, B.G.
History
DepositionSep 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 13, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_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 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6633
Polymers16,1711
Non-polymers4912
Water2,720151
1
A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE
hetero molecules

A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE
hetero molecules

A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9899
Polymers48,5143
Non-polymers1,4746
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area9230 Å2
ΔGint-98 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.596, 60.596, 63.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-188-

HOH

21A-289-

HOH

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Components

#1: Protein DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE


Mass: 16171.373 Da / Num. of mol.: 1 / Fragment: dUTPase (catalytic) domain, UNP residues 608-759 / Mutation: N83K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mason-pfizer monkey virus / Gene: gag-pro / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O92810, UniProt: P07570*PLUS, dUTP diphosphatase
#2: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8034 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 26, 2005 / Details: BENT, VERTICALLY FOCUSING MIRROR
RadiationMonochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8034 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 17501 / Num. obs: 17501 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rsym value: 0.04 / Net I/σ(I): 17
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2371 / Rsym value: 0.32 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345data collection
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: rigid body refinement
Starting model: PDB entry 2D4L

2d4l


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.756 / SU ML: 0.067 / Isotropic thermal model: TLS and isotropic individual / Cross valid method: THROUGHOUT / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19733 966 5.5 %RANDOM
Rwork0.16698 ---
obs0.16866 16534 99.22 %-
all-16534 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.095 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms823 0 29 151 1003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023875
X-RAY DIFFRACTIONr_angle_refined_deg1.9572.0991202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.9115.168119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47125.90922
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88515141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.465153
X-RAY DIFFRACTIONr_chiral_restr0.1230.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02612
X-RAY DIFFRACTIONr_nbd_refined0.2220.2394
X-RAY DIFFRACTIONr_nbtor_refined0.320.2613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2117
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.228
X-RAY DIFFRACTIONr_mcbond_it2.9084580
X-RAY DIFFRACTIONr_mcangle_it3.8356937
X-RAY DIFFRACTIONr_scbond_it5.3588319
X-RAY DIFFRACTIONr_scangle_it7.40120263
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 91 -
Rwork0.271 1198 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: 2.854 Å / Origin y: 58.549 Å / Origin z: 30.333 Å
111213212223313233
T-0.0962 Å20.0076 Å2-0.0096 Å2--0.1347 Å20.0224 Å2---0.0599 Å2
L0.7728 °2-0.0038 °2-0.4889 °2-0.8869 °20.2036 °2--2.1261 °2
S0.0105 Å °-0.0832 Å °-0.1243 Å °-0.0402 Å °0.0425 Å °-0.0327 Å °0.0794 Å °0.1594 Å °-0.053 Å °

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