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- PDB-3tq4: Crystal structure of M-PMV dUTPase with a mixed population of sub... -

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Basic information

Entry
Database: PDB / ID: 3tq4
TitleCrystal structure of M-PMV dUTPase with a mixed population of substrate (dUPNPP) and post-inversion product (dUMP) in the active sites
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 / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / 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 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 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_alt_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,0775
Polymers16,1551
Non-polymers9224
Water1,838102
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)51,23115
Polymers48,4663
Non-polymers2,76512
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 area11710 Å2
ΔGint-78 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.564, 60.564, 64.018
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE


Mass: 16155.373 Da / Num. of mol.: 1 / Fragment: dUTPase (catalytic) domain, UNP residues 608-759 / Mutation: N1K
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

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Non-polymers , 5 types, 106 molecules

#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
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: X11 / Wavelength: 0.8028, 1.0720
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 4, 2004 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.80281
21.0721
ReflectionResolution: 1.6→52.41 Å / Num. all: 17234 / Num. obs: 17234 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.072 / Net I/σ(I): 13.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2584 / Rsym value: 0.403 / % possible all: 97

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0005phasing
RefinementMethod to determine structure: rigid body refinement
Starting model: PDB entry 2D4L

2d4l


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.024 / SU ML: 0.073 / Isotropic thermal model: TLS and isotropic individual / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 929 5.4 %RANDOM
Rwork0.1722 ---
obs0.1732 16305 97.61 %-
all-17234 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 55.29 Å2 / Biso mean: 25.406 Å2 / Biso min: 6.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.49 Å20 Å2
2--0.99 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 57 102 974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022928
X-RAY DIFFRACTIONr_angle_refined_deg1.9522.0771286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0315125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.38726.53826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5415151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.211152
X-RAY DIFFRACTIONr_chiral_restr0.1280.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02653
X-RAY DIFFRACTIONr_nbd_refined0.2290.2381
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1670.21
X-RAY DIFFRACTIONr_mcbond_it1.5021.5594
X-RAY DIFFRACTIONr_mcangle_it2.8786962
X-RAY DIFFRACTIONr_scbond_it4.2616363
X-RAY DIFFRACTIONr_scangle_it5.3216318
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 64 -
Rwork0.293 1188 -
all-1252 -
obs--96.16 %
Refinement TLS params.Method: refined / Origin x: 2.7342 Å / Origin y: 58.4359 Å / Origin z: 30.2099 Å
111213212223313233
T-0.0327 Å20.0108 Å2-0.0136 Å2--0.0812 Å20.0384 Å2---0.0138 Å2
L1.0287 °20.2196 °2-0.6983 °2-1.186 °20.127 °2--2.7538 °2
S-0.0025 Å °-0.0777 Å °-0.1671 Å °0.0235 Å °0.015 Å °-0.0031 Å °0.14 Å °0.1644 Å °-0.0125 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 136
2X-RAY DIFFRACTION1A777
3X-RAY DIFFRACTION1A154 - 155

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