[English] 日本語
Yorodumi
- PDB-3urb: Crystal Structure of PTE mutant H254G/H257W/L303T/M317L/I106C/F13... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3urb
TitleCrystal Structure of PTE mutant H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H
ComponentsParathion hydrolase
KeywordsHYDROLASE / metalloenzyme / TIM barrel / nerve agents / phosphotriesterase
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / 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
: / DIETHYL HYDROGEN PHOSPHATE / IMIDAZOLE / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsTsai, P. / Fox, N.G. / Li, Y. / Barondeau, D.P. / Raushel, F.M.
CitationJournal: Biochemistry / Year: 2012
Title: Enzymes for the homeland defense: optimizing phosphotriesterase for the hydrolysis of organophosphate nerve agents.
Authors: Tsai, P.C. / Fox, N. / Bigley, A.N. / Harvey, S.P. / Barondeau, D.P. / Raushel, F.M.
History
DepositionNov 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Sep 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Parathion hydrolase
B: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5389
Polymers70,9252
Non-polymers6137
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-50 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.468, 86.396, 88.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1537-

HOH

-
Components

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 35462.254 Da / Num. of mol.: 2 / Fragment: UNP residues 35-361
Mutation: H254G/H257W/L303T/M317L/I106C/F132I/L271I/K185R/I274N/A80V/R67H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A434, aryldialkylphosphatase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-DPF / DIETHYL HYDROGEN PHOSPHATE


Mass: 154.102 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H11O4P
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 uL 7.8 mg/mL protein + 2 uL seeding solution (24% PEG5000 MME, 4% dioxane, 1.0 mM cobalt chloride, 100 mM diethylphosphate, 0.1 M imidazole, pH 7.0) over 500 uL precipitating agent (22% ...Details: 2 uL 7.8 mg/mL protein + 2 uL seeding solution (24% PEG5000 MME, 4% dioxane, 1.0 mM cobalt chloride, 100 mM diethylphosphate, 0.1 M imidazole, pH 7.0) over 500 uL precipitating agent (22% PEG5000 MME), VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 25, 2009
RadiationMonochromator: Si(111), Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 64147 / Num. obs: 64147 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.5 % / Biso Wilson estimate: 26.3 Å2 / Rsym value: 0.065 / Net I/σ(I): 44.6
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 17.3 / Num. unique all: 6095 / Rsym value: 0.195 / % possible all: 95.8

-
Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HZY

1hzy


Resolution: 1.77→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 3247 5.1 %RANDOM
Rwork0.2156 60895 --
obs-64142 99.8 %-
Solvent computationBsol: 27.9089 Å2
Displacement parametersBiso max: 78.9 Å2 / Biso mean: 31.1278 Å2 / Biso min: 11.15 Å2
Baniso -1Baniso -2Baniso -3
1--4.591 Å20 Å20 Å2
2--9.484 Å20 Å2
3----4.893 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 27 559 5506
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_d1.591
X-RAY DIFFRACTIONc_mcbond_it1.1661.5
X-RAY DIFFRACTIONc_scbond_it1.6762
X-RAY DIFFRACTIONc_mcangle_it1.8112
X-RAY DIFFRACTIONc_scangle_it2.4192.5
LS refinement shellResolution: 1.77→1.83 Å
RfactorNum. reflection
Rfree0.334 302
Rwork0.293 -
obs-5966
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein.gfp.paramCNS_TOPPAR:protein.gfp.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5co.param.txtco.top.txt

+
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