[English] 日本語
Yorodumi
- PDB-1dut: FIV DUTP PYROPHOSPHATASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dut
TitleFIV DUTP PYROPHOSPHATASE
ComponentsDUTP PYROPHOSPHATASE
KeywordsASPARTYL PROTEASE / POLYPROTEIN / HYDROLASE / ENDONUCLEASE / RNA-DIRECTED DNA POLYMERASE / NUCLEOTIDE METABOLISM / ACID ANHYDRIDE HYDROLASE
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase ...dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / symbiont entry into host cell / magnesium ion binding / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Distorted Sandwich ...Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Distorted Sandwich / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesFeline immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsPrasad, G.S. / Stura, E.A. / Mcree, D.E. / Laco, G.S. / Hasselkus-Light, C. / Elder, J.H. / Stout, C.D.
CitationJournal: Protein Sci. / Year: 1996
Title: Crystal structure of dUTP pyrophosphatase from feline immunodeficiency virus.
Authors: Prasad, G.S. / Stura, E.A. / McRee, D.E. / Laco, G.S. / Hasselkus-Light, C. / Elder, J.H. / Stout, C.D.
History
DepositionSep 15, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Mar 21, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.pdbx_collection_date / _pdbx_database_status.process_site
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: DUTP PYROPHOSPHATASE
B: DUTP PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7884
Polymers28,7402
Non-polymers492
Water1,29772
1
A: DUTP PYROPHOSPHATASE
hetero molecules

A: DUTP PYROPHOSPHATASE
hetero molecules

A: DUTP PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1826
Polymers43,1093
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8790 Å2
ΔGint-71 kcal/mol
Surface area14530 Å2
MethodPISA, PQS
2
B: DUTP PYROPHOSPHATASE
hetero molecules

B: DUTP PYROPHOSPHATASE
hetero molecules

B: DUTP PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1826
Polymers43,1093
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9200 Å2
ΔGint-93 kcal/mol
Surface area13850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.800, 79.800, 86.950
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-134-

MG

21B-134-

MG

-
Components

#1: Protein DUTP PYROPHOSPHATASE / DUTPASE / DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE


Mass: 14369.802 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Genus: Lentivirus / Strain: (isolate Petaluma) / Cell line (production host): TN5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P16088, dUTP diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 22.5 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
129 mMTris-HCl1drop
22.9 mM1dropMgCl2
31.2 mM2-mercaptoethanol1drop
41.2 mg/mlenzyme1drop
55.4 %MPEG50001drop
642 mMsodium cacodylate1drop
713 %MPEG50001reservoir
8100 mMsodium cacodylate1reservoir

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionNum. obs: 116665 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 4.96 % / Rmerge(I) obs: 0.064
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 23522 / Num. measured all: 116665

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data reduction
X-PLOR3.1phasing
RefinementResolution: 1.9→7 Å / σ(F): 0
Details: DUTP PYROPHOSPHATASE IS AN INTERDIGITATED, FUNCTIONAL TRIMER. IN THE STRUCTURE ONE TRIMER (CHAIN A) LIES ON A CRYSTALLOGRAPHIC 6(3) AXIS AND ANOTHER TRIMER (CHAIN B) LIES ON THE ...Details: DUTP PYROPHOSPHATASE IS AN INTERDIGITATED, FUNCTIONAL TRIMER. IN THE STRUCTURE ONE TRIMER (CHAIN A) LIES ON A CRYSTALLOGRAPHIC 6(3) AXIS AND ANOTHER TRIMER (CHAIN B) LIES ON THE CRYSTALLOGRAPHIC THREE-FOLD AXIS. THE SPACE GROUP IS P6(3) WITH 2 MONOMERS (CHAINS A AND B) IN THE ASYMMETRIC UNIT. EACH MONOMER CONSISTS OF 117 RESIDUES AND A MG2+ ION COORDINATED ON THE THREE-FOLD AXIS OF THE TRIMER. THE C-TERMINAL 16 AMINO-ACIDS OF THE KNOWN PRIMARY SEQUENCE ARE DISORDERED IN EACH UNIQUE MONOMER.
RfactorNum. reflection
Rfree0.249 -
Rwork0.209 -
obs0.209 23522
Refinement stepCycle: LAST / Resolution: 1.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 2 72 1848
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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