[English] 日本語
Yorodumi
- PDB-5w3u: Crystal structure of SsoPox AsB5 mutant (V27A-I76T-Y97W-Y99F-L130... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w3u
TitleCrystal structure of SsoPox AsB5 mutant (V27A-I76T-Y97W-Y99F-L130P-L226V)
ComponentsAryldialkylphosphatase
KeywordsHYDROLASE / lactonase / phosphotriesterase / mutants / quorum sensing / organophosphate / organophosphorous / insecticides.
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / : / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsHiblot, J. / Gotthard, G. / Jacquet, P. / Daude, D. / Bergonzi, C. / Chabriere, E. / Elias, M.
CitationJournal: Sci Rep / Year: 2017
Title: Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase.
Authors: Jacquet, P. / Hiblot, J. / Daude, D. / Bergonzi, C. / Gotthard, G. / Armstrong, N. / Chabriere, E. / Elias, M.
History
DepositionJun 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aryldialkylphosphatase
B: Aryldialkylphosphatase
C: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,36118
Polymers142,3794
Non-polymers98214
Water1,27971
1
A: Aryldialkylphosphatase
B: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,75710
Polymers71,1902
Non-polymers5688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-19 kcal/mol
Surface area22420 Å2
MethodPISA
2
C: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6038
Polymers71,1902
Non-polymers4146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-18 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.930, 105.950, 152.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Aryldialkylphosphatase / Paraoxonase / SsoPox / Phosphotriesterase-like lactonase


Mass: 35594.766 Da / Num. of mol.: 4 / Mutation: V27A-I76T-Y97W-Y99F-L130P-L226V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97VT7, aryldialkylphosphatase

-
Non-polymers , 5 types, 85 molecules

#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20-30 % (w/v) PEG 8000 and 50 mM Tris-HCl buffer (pH 8)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→49.64 Å / Num. obs: 47092 / % possible obs: 99.5 % / Redundancy: 4.38 % / Net I/σ(I): 12.84

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 2.5→49.64 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 30.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 2355 5 %RANDOM
Rwork0.2122 ---
obs0.2152 47089 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9362 0 42 71 9475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059575
X-RAY DIFFRACTIONf_angle_d0.84912915
X-RAY DIFFRACTIONf_dihedral_angle_d20.8325753
X-RAY DIFFRACTIONf_chiral_restr0.0531452
X-RAY DIFFRACTIONf_plane_restr0.0051666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55110.41370.35022608X-RAY DIFFRACTION100
2.5511-2.60650.36411370.33032605X-RAY DIFFRACTION100
2.6065-2.66720.35951370.30822590X-RAY DIFFRACTION99
2.6672-2.73390.35431350.3052577X-RAY DIFFRACTION98
2.7339-2.80780.40311370.29912605X-RAY DIFFRACTION100
2.8078-2.89040.35491380.27542618X-RAY DIFFRACTION100
2.8904-2.98370.36371370.26232599X-RAY DIFFRACTION100
2.9837-3.09030.32211380.24282623X-RAY DIFFRACTION100
3.0903-3.2140.31531380.23472619X-RAY DIFFRACTION100
3.214-3.36030.33371370.23842601X-RAY DIFFRACTION99
3.3603-3.53740.30671370.22542605X-RAY DIFFRACTION99
3.5374-3.75890.24491390.20862640X-RAY DIFFRACTION100
3.7589-4.0490.25481390.20242642X-RAY DIFFRACTION100
4.049-4.45630.24281400.17422657X-RAY DIFFRACTION100
4.4563-5.10050.23261390.17442652X-RAY DIFFRACTION99
5.1005-6.4240.26681420.21062696X-RAY DIFFRACTION99
6.424-49.65470.21511480.17482797X-RAY DIFFRACTION99
Refinement TLS params.

S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.03290.35360.41931.20650.58636.03830.2072-0.0670.02790.11440.0215-0.12450.6176-0.18290.2398-0.02480.05870.32570.00210.4312-22.8962-10.263417.6102
21.0184-0.11090.63431.24190.41895.35850.00710.06580.0204-0.37910.02520.00581.50480.09560.40140.0617-0.03680.34270.04480.3472-21.9654-17.7403-21.5384
31.6734-1.0194-0.99173.21180.33994.8681-0.005-0.0263-0.21730.3681-0.3180.2019-0.3219-0.00870.4013-0.02190.01060.406-0.05240.4706-59.284410.400827.0928
40.8599-0.74880.10492.7415-1.01173.3208-0.1001-0.12140.0588-0.38430.21730.4503-0.2466-0.41120.6260.1565-0.06670.4570.00790.4986-67.278717.9232-11.8078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:314 OR RESID 401:404 ) )A2 - 314
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:314 OR RESID 401:404 ) )A401 - 404
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 1:314 OR RESID 401:404 ) )B1 - 314
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 1:314 OR RESID 401:404 ) )B401 - 404
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 1:314 OR RESID 401:403 ) )C1 - 314
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 1:314 OR RESID 401:403 ) )C401 - 403
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID 1:314 OR RESID 401:403 ) )D1 - 314
8X-RAY DIFFRACTION4( CHAIN D AND ( RESID 1:314 OR RESID 401:403 ) )D401 - 403

+
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