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- PDB-2d4m: Crystal Structure of apo M-PMV dUTPase -

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Basic information

Entry
Database: PDB / ID: 2d4m
TitleCrystal Structure of apo 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 process / viral nucleocapsid / structural constituent of virion / aspartic-type endopeptidase activity / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / 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 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic 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
: / Gag-Pro polyprotein
Similarity search - Component
Biological speciesMason-Pfizer monkey virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 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 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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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
Water2,648147
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 area6550 Å2
ΔGint-59 kcal/mol
Surface area13620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.191, 61.191, 63.310
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-240-

HOH

21A-370-

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: GenBank: 40018527, UniProt: P07570*PLUS, dUTP diphosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
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: X13 / Wavelength: 0.8031 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 4, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8031 Å / Relative weight: 1
ReflectionResolution: 1.83→53 Å / Num. all: 11637 / Num. obs: 11637 / % possible obs: 97.37 % / Observed criterion σ(I): -3 / Redundancy: 2.74 % / Biso Wilson estimate: 33.38 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.074 / Net I/σ(I): 8.85
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.66 / Num. unique all: 1804 / Rsym value: 0.4 / % possible all: 95.04

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
RefinementStarting model: 2D4L

2d4l


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.724 / SU ML: 0.087 / Isotropic thermal model: TLS and isotropic individual / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, rigid body refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.19193 611 5.4 %RANDOM
Rwork0.16022 ---
all0.16194 10739 --
obs0.16194 10739 98.01 %-
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: 32.784 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 0 147 959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022854
X-RAY DIFFRACTIONr_angle_refined_deg1.8622.0091179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.0985.16125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.37526.81822
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38615141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.842151
X-RAY DIFFRACTIONr_chiral_restr0.1230.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02614
X-RAY DIFFRACTIONr_nbd_refined0.230.2386
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.224
X-RAY DIFFRACTIONr_mcbond_it3.2324588
X-RAY DIFFRACTIONr_mcangle_it4.3826954
X-RAY DIFFRACTIONr_scbond_it8.75820284
X-RAY DIFFRACTIONr_scangle_it11.38350219
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 40 -
Rwork0.244 811 -
obs-851 99.42 %

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