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- PDB-2d4l: Crystal structure of truncated in C-terminal M-PMV dUTPase -

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Basic information

Entry
Database: PDB / ID: 2d4l
TitleCrystal structure of truncated in C-terminal M-PMV dUTPase
ComponentsDU
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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / 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
Biological speciesMason-Pfizer monkey virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsNemeth, V. / Barabas, O. / Vertessy, G.B.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.
Authors: Nemeth-Pongracz, V. / Barabas, O. / Fuxreiter, M. / Simon, I. / Pichova, I. / Rumlova, M. / Zabranska, H. / Svergun, D. / Petoukhov, M. / Harmat, V. / Klement, E. / Hunyadi-Gulyas, E. / ...Authors: Nemeth-Pongracz, V. / Barabas, O. / Fuxreiter, M. / Simon, I. / Pichova, I. / Rumlova, M. / Zabranska, H. / Svergun, D. / Petoukhov, M. / Harmat, V. / Klement, E. / Hunyadi-Gulyas, E. / Medzihradszky, K.F. / Konya, E. / Vertessy, B.G.
History
DepositionOct 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 20, 2011Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.8Oct 23, 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: DU


Theoretical massNumber of molelcules
Total (without water)16,1711
Polymers16,1711
Non-polymers00
Water2,234124
1
A: DU

A: DU

A: DU


Theoretical massNumber of molelcules
Total (without water)48,5143
Polymers48,5143
Non-polymers00
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 area6510 Å2
ΔGint-58 kcal/mol
Surface area14280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.163, 61.163, 64.167
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-241-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: 2-y,2+x-y,z and -x+y,2-x,z

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Components

#1: Protein DU / Deoxyuridine 5'-Triphosphate Nucleotido Hydrolase


Mass: 16171.373 Da / Num. of mol.: 1 / Fragment: residues 83-234 / Mutation: N83K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mason-Pfizer monkey virus / Genus: Betaretrovirus / Gene: gag-pro / Plasmid: pET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07570, dUTP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
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 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 19, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.7→53 Å / Num. all: 14813 / Num. obs: 14813 / % possible obs: 98.34 % / Observed criterion σ(I): -3 / Redundancy: 3.08 % / Biso Wilson estimate: 33.811 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.031 / Net I/σ(I): 21.15
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 3.33 / Num. unique all: 2308 / Rsym value: 0.44 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
RefinementStarting model: 2AKV

2akv
PDB Unreleased entry


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 4.977 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS and isotropic individual / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, rigid body refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.17888 800 5.4 %RANDOM
Rwork0.1623 ---
all0.1632 14013 --
obs0.1632 14013 98.34 %-
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: 31.803 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20.61 Å20 Å2
2--1.22 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 0 124 952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022869
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9482.0071192
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.2025.16125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.50627.08324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57515152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.046152
X-RAY DIFFRACTIONr_chiral_restr0.1410.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02622
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2366
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.2615
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3382589
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.27420955
X-RAY DIFFRACTIONr_scbond_it12.77650298
X-RAY DIFFRACTIONr_scangle_it15.0650232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 61 -
Rwork0.282 1016 -
obs-1077 97.82 %
Refinement TLS params.Method: refined / Origin x: 2.6934 Å / Origin y: 59.2597 Å / Origin z: 30.4909 Å
111213212223313233
T-0.0407 Å20.0145 Å2-0.0126 Å2--0.0711 Å20.0239 Å2---0.0174 Å2
L0.939 °20.1287 °2-0.5426 °2-1.2128 °20.2015 °2--2.0859 °2
S0.0233 Å °-0.092 Å °-0.1518 Å °0.0022 Å °0.0293 Å °-0.0501 Å °0.1283 Å °0.1388 Å °-0.0526 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA106 - 21924 - 137
2X-RAY DIFFRACTION1AB235 - 3581 - 124

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