[English] 日本語
Yorodumi
- PDB-7p85: Engineered phosphotriesterase BdPTE 10-2-C3(C59V/C227V) in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p85
TitleEngineered phosphotriesterase BdPTE 10-2-C3(C59V/C227V) in complex with ethyl-4-methylbenzylphosphonate
ComponentsParathion hydrolase
KeywordsHYDROLASE / BIOSCAVENGER / ENZYME ENGINEERING / ORGANOPHOSPHATE HYDROLASE / ORGANOPHOSPHOROUS COMPOUND / PHOSPHOTRIESTERASE
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 hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
ethyl-4-methylbenzylphosphonate / FORMIC ACID / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsEichinger, A. / Skerra, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other governmentBundesamt fuer Ausruestung, Informationstechnik und Nutzung der Bundeswehr, E/U2AD/GD003/GF560 Germany
CitationJournal: Biochemistry / Year: 2023
Title: Structural and Functional Analysis of a Highly Active Designed Phosphotriesterase for the Detoxification of Organophosphate Nerve Agents Reveals an Unpredicted Conformation of the Active Site Loop.
Authors: Job, L. / Kohler, A. / Eichinger, A. / Testanera, M. / Escher, B. / Worek, F. / Skerra, A.
History
DepositionJul 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,64011
Polymers37,6841
Non-polymers95610
Water4,522251
1
A: Parathion hydrolase
hetero molecules

A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,28022
Polymers75,3692
Non-polymers1,91120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area5640 Å2
ΔGint-83 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.298, 69.298, 186.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-730-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 37684.441 Da / Num. of mol.: 1
Mutation: C59V, K77A, A80M, R118E, F132E, T173N, K185R, A203D, S222D, C227V, D233G, S238D, H254G, A270S, L271W, I274N, M293V, Y309W, R319S, P342S, G348T, T352E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A434, aryldialkylphosphatase

-
Non-polymers , 6 types, 261 molecules

#2: Chemical ChemComp-5ZG / ethyl-4-methylbenzylphosphonate


Mass: 214.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15O3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: ammonium sulfate, glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 27, 2019 / Details: Si mirror
RadiationMonochromator: Si 111 double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.467→64.977 Å / Num. all: 78996 / Num. obs: 78996 / % possible obs: 100 % / Redundancy: 22.5 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.201 / Rsym value: 0.196 / Net I/av σ(I): 1.8 / Net I/σ(I): 10.2 / Num. measured all: 1773620
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.47-1.5523.30.9640.8264395113640.2010.9850.9643.7100
1.55-1.6421.90.7591234942107320.1640.7770.7594.5100
1.64-1.7521.70.5821.2219427101160.1260.5960.5825.8100
1.75-1.8924.50.431.523202594620.0870.4390.438.3100
1.89-2.0723.40.295220424587280.0620.3020.29511.1100
2.07-2.32200.2032.815934979520.0460.2090.20313.1100
2.32-2.6822.10.1643.115586970560.0350.1680.16415.7100
2.68-3.2823.50.1363.414137960260.0280.1390.13618.5100
3.28-4.6419.70.1173.59376547510.0270.1210.11719.4100
4.64-49.00124.30.14236822428090.0290.1450.1422199.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.18 Å49 Å
Translation6.18 Å49 Å

-
Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSC

1psc


Resolution: 1.47→49.05 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.683 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0504 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1744 3863 4.9 %RANDOM
Rwork0.1573 ---
obs0.1581 75013 99.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.07 Å2 / Biso mean: 17.411 Å2 / Biso min: 8.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.47→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 52 251 2859
Biso mean--25.28 26.54 -
Num. residues----331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132720
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172606
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.6363706
X-RAY DIFFRACTIONr_angle_other_deg0.5011.5735972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.43320.272147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16815439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7631528
X-RAY DIFFRACTIONr_chiral_restr0.0880.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0570.023113
X-RAY DIFFRACTIONr_gen_planes_other0.0490.02651
LS refinement shellResolution: 1.47→1.505 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 270 -
Rwork-5490 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.718 Å / Origin y: -33.493 Å / Origin z: -10.048 Å
111213212223313233
T0.0475 Å20.0058 Å2-0.0058 Å2-0.0255 Å20.0119 Å2--0.0214 Å2
L0.1178 °2-0.179 °20.0406 °2-0.3447 °2-0.1893 °2--0.3425 °2
S-0.0229 Å °-0.0309 Å °-0.0096 Å °0.014 Å °0.0584 Å °0.0252 Å °-0.0317 Å °-0.0374 Å °-0.0355 Å °

+
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