[English] 日本語
Yorodumi
- PDB-1pta: THREE-DIMENSIONAL STRUCTURE OF PHOSPHOTRIESTERASE: AN ENZYME CAPA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pta
TitleTHREE-DIMENSIONAL STRUCTURE OF PHOSPHOTRIESTERASE: AN ENZYME CAPABLE OF DETOXIFYING ORGANOPHOSPHATE NERVE AGENTS
ComponentsPHOSPHOTRIESTERASE
KeywordsHYDROLASE (ORGANOPHOSPHATE-DEGRADING)
Function / homology
Function and homology information


aryldialkylphosphatase activity / aryldialkylphosphatase / catabolic process / zinc ion binding / plasma membrane
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel ...Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsBenning, M. / Holden, H.M.
Citation
Journal: Biochemistry / Year: 1994
Title: Three-dimensional structure of phosphotriesterase: an enzyme capable of detoxifying organophosphate nerve agents.
Authors: Benning, M.M. / Kuo, J.M. / Raushel, F.M. / Holden, H.M.
#1: Journal: Biochemistry / Year: 1995
Title: Three-Dimensional Structure of the Binuclear Metal Center of Phosphotriesterase
Authors: Benning, M.M. / Kuo, J.M. / Raushel, F.M. / Holden, H.M.
History
DepositionJul 7, 1994Processing site: BNL
Revision 1.0Dec 1, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHOTRIESTERASE


Theoretical massNumber of molelcules
Total (without water)35,4871
Polymers35,4871
Non-polymers00
Water2,324129
1
A: PHOSPHOTRIESTERASE

A: PHOSPHOTRIESTERASE


Theoretical massNumber of molelcules
Total (without water)70,9732
Polymers70,9732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3120 Å2
ΔGint-22 kcal/mol
Surface area25620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.200, 93.700, 45.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PHOSPHOTRIESTERASE


Mass: 35486.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brevundimonas diminuta (bacteria)
References: UniProt: P0A434, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlprotein 1drop
210 mMHEPES1drop
39 %PEG80001reservoir
4100 mMbicine1reservoir
55 mM1reservoirNaN3
61 M1reservoirLiCl

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.09 Å / Lowest resolution: 100 Å / Num. obs: 21816 / % possible obs: 93 % / Num. measured all: 93927 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
Highest resolution: 2.09 Å / Lowest resolution: 2.2 Å / % possible obs: 88 % / Num. unique obs: 2551 / Num. measured obs: 8985 / Rmerge(I) obs: 0.171

-
Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.1→30.1 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.18 20330 93 %
Refinement stepCycle: LAST / Resolution: 2.1→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 0 129 2568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.32
X-RAY DIFFRACTIONt_dihedral_angle_d17.1
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006
X-RAY DIFFRACTIONt_gen_planes0.012
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.1

+
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