[English] 日本語
Yorodumi
- PDB-3tq3: Crystal structure of M-PMV dUTPase with a mixed population of sub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tq3
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 / 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 / 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: 1.85 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,9554
Polymers16,1551
Non-polymers8003
Water1,78399
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)50,86512
Polymers48,4663
Non-polymers2,3999
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 area10880 Å2
ΔGint-101 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.594, 60.594, 64.146
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

-
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: 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.55 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8124 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 14, 2003 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8124 Å / Relative weight: 1
ReflectionResolution: 1.85→52.49 Å / Num. all: 11478 / Num. obs: 11478 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rsym value: 0.078 / Net I/σ(I): 20.2
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 5 / Num. unique all: 1821 / Rsym value: 0.539 / % possible all: 99.7

-
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: 1.85→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.208 / SU ML: 0.07 / Isotropic thermal model: TLS and isotropic individual / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1688 614 5.3 %RANDOM
Rwork0.1538 ---
obs0.1546 10863 99.84 %-
all-11477 --
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: 52.67 Å2 / Biso mean: 25.398 Å2 / Biso min: 13.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms825 0 49 99 973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022919
X-RAY DIFFRACTIONr_angle_refined_deg1.8122.071270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67125.625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47215151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.618153
X-RAY DIFFRACTIONr_chiral_restr0.1290.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02646
X-RAY DIFFRACTIONr_nbd_refined0.2120.2378
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.282
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.218
X-RAY DIFFRACTIONr_mcbond_it1.1151.5593
X-RAY DIFFRACTIONr_mcangle_it1.7512952
X-RAY DIFFRACTIONr_scbond_it2.7153360
X-RAY DIFFRACTIONr_scangle_it3.9584.5314
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 36 -
Rwork0.213 819 -
all-855 -
obs--99.65 %
Refinement TLS params.Method: refined / Origin x: 2.4667 Å / Origin y: 58.4802 Å / Origin z: 30.3162 Å
111213212223313233
T-0.0383 Å20.0035 Å2-0.0079 Å2--0.0712 Å20.038 Å2---0.0296 Å2
L1.0541 °20.1926 °2-0.6254 °2-1.1755 °20.2064 °2--2.0741 °2
S0.0021 Å °-0.0969 Å °-0.1571 Å °0.0372 Å °-0.0005 Å °-0.0088 Å °0.1085 Å °0.1308 Å °-0.0016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 137
2X-RAY DIFFRACTION1A153 - 154
3X-RAY DIFFRACTION1A777

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more