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- PDB-3tta: Crystal structure of M-PMV DUTPASE relaxed end-product (dUMP) complex -

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Basic information

Entry
Database: PDB / ID: 3tta
TitleCrystal structure of M-PMV DUTPASE relaxed end-product (dUMP) 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'-MONOPHOSPHATE / Gag-Pro polyprotein / Gag-Pro polyprotein
Similarity search - Component
Biological speciesMASON-PFIZER MONKEY VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 2 Å
AuthorsNemeth, V. / Barabas, O. / Vertessy, G.B.
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 14, 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 1.2Sep 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 / 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 / _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)16,4642
Polymers16,1551
Non-polymers3081
Water1,72996
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)49,3916
Polymers48,4663
Non-polymers9253
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 area8250 Å2
ΔGint-59 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.884, 60.884, 63.867
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-160-

HOH

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Components

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


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
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: BW7B / Wavelength: 0.8128 / Wavelength: 0.843 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 2005 / 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
10.81281
20.8431
ReflectionResolution: 2→20 Å / Num. all: 8979 / Num. obs: 8979 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rsym value: 0.06 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1239 / Rsym value: 0.493 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MAR345data collection
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0005phasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: PDB ENTRY 2D4L

2d4l


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 9.47 / SU ML: 0.121 / Isotropic thermal model: TLS and isotropic individual / Cross valid method: THROUGHOUT / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20407 482 5.4 %RANDOM
Rwork0.16241 ---
obs0.16473 8493 97.86 %-
all-8493 --
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 mean: 34.695 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20.91 Å20 Å2
2--1.81 Å20 Å2
3----2.72 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 20 96 930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022860
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8852.0371180
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1885116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.51225.90922
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12615142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.503152
X-RAY DIFFRACTIONr_chiral_restr0.1210.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02608
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.2364
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.2592
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5272576
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6563927
X-RAY DIFFRACTIONr_scbond_it7.39310308
X-RAY DIFFRACTIONr_scangle_it10.28635251
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 35 -
Rwork0.241 646 -
obs--98.7 %
Refinement TLS params.Method: refined / Origin x: 2.731 Å / Origin y: 58.8764 Å / Origin z: 30.3144 Å
111213212223313233
T-0.0549 Å20.014 Å2-0.0154 Å2--0.0779 Å20.029 Å2---0.0217 Å2
L0.9117 °20.1538 °2-0.5532 °2-1.6516 °2-0.0391 °2--2.7534 °2
S-0.0303 Å °-0.1362 Å °-0.1941 Å °0.0321 Å °0.0085 Å °-0.0776 Å °0.1847 Å °0.2265 Å °0.0218 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 136
2X-RAY DIFFRACTION1A153 - 246

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