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- PDB-2d4n: Crystal Structure of M-PMV dUTPase complexed with dUPNPP, substra... -

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Basic information

Entry
Database: PDB / ID: 2d4n
TitleCrystal Structure of M-PMV dUTPase complexed with dUPNPP, substrate analogue
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
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / : / Gag-Pro polyprotein
Similarity search - Component
Biological speciesMason-Pfizer monkey virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 1.53 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: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 20, 2011Group: Database references / Non-polymer description
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 / 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.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 1.6Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7694
Polymers16,1551
Non-polymers6143
Water2,468137
1
A: DU
hetero molecules

A: DU
hetero molecules

A: DU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,30712
Polymers48,4663
Non-polymers1,8419
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 area10160 Å2
ΔGint-84 kcal/mol
Surface area13550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.071, 61.071, 64.357
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-1001-

TRS

21A-1001-

TRS

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: 16155.373 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: Chemical ChemComp-MG / MAGNESIUM ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
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: X11 / Wavelength: 0.8128 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8128 Å / Relative weight: 1
ReflectionResolution: 1.52→52.93 Å / Num. all: 20787 / Num. obs: 20787 / % possible obs: 98.72 % / Observed criterion σ(I): -3 / Redundancy: 2.66 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.057 / Net I/σ(I): 12.34
Reflection shellResolution: 1.52→1.61 Å / Redundancy: 2.13 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.86 / Num. unique all: 3282 / Rsym value: 0.334 / % possible all: 98.23

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: rigid body refinement
Starting model: 2D4L

2d4l


Resolution: 1.53→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.454 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS and isotropic individual / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, rigid body refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.18717 1097 5.4 %from starting model
Rwork0.16443 ---
all0.16566 19296 --
obs0.16566 19296 98.97 %-
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: 22.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.3 Å20 Å2
2--0.61 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 37 137 1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022910
X-RAY DIFFRACTIONr_angle_refined_deg1.9112.051255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7525124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35325.76926
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1115153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.573153
X-RAY DIFFRACTIONr_chiral_restr0.1410.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02645
X-RAY DIFFRACTIONr_nbd_refined0.2350.2395
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2100
X-RAY DIFFRACTIONr_metal_ion_refined0.0020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.222
X-RAY DIFFRACTIONr_mcbond_it2.6243596
X-RAY DIFFRACTIONr_mcangle_it3.88310964
X-RAY DIFFRACTIONr_scbond_it8.09750341
X-RAY DIFFRACTIONr_scangle_it10.45750286
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 79 -
Rwork0.245 1409 -
obs-1488 99.87 %
Refinement TLS params.Method: refined / Origin x: 2.4987 Å / Origin y: 59.1533 Å / Origin z: 30.661 Å
111213212223313233
T-0.0165 Å20.0045 Å2-0.0033 Å2--0.0444 Å20.0081 Å2---0.0041 Å2
L0.4966 °2-0.0433 °2-0.0637 °2-0.6739 °20.1368 °2--1.0476 °2
S0.0067 Å °-0.024 Å °-0.0736 Å °-0.0111 Å °0.031 Å °-0.0199 Å °0.0919 Å °0.0691 Å °-0.0377 Å °

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