[English] 日本語
Yorodumi
- PDB-4xaf: Cycles of destabilization and repair underlie evolutionary transi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xaf
TitleCycles of destabilization and repair underlie evolutionary transitions in enzymes
ComponentsPhosphotriesterase variant PTE-R1
KeywordsHYDROLASE / dynamics / evolution / phosphotriesterase
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / 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
CACODYLATE ION / Phosphotriesterase variant PTE-R1
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsJackson, C.J. / Campbell, E. / Kaltenbach, M. / Tokuriki, N.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: The role of protein dynamics in the evolution of new enzyme function.
Authors: Campbell, E. / Kaltenbach, M. / Correy, G.J. / Carr, P.D. / Porebski, B.T. / Livingstone, E.K. / Afriat-Jurnou, L. / Buckle, A.M. / Weik, M. / Hollfelder, F. / Tokuriki, N. / Jackson, C.J.
History
DepositionDec 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Oct 26, 2016Group: Database references
Revision 1.4Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _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
Revision 1.5Nov 15, 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: Phosphotriesterase variant PTE-R1
G: Phosphotriesterase variant PTE-R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,92210
Polymers72,1502
Non-polymers7728
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-156 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.687, 85.733, 88.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Phosphotriesterase variant PTE-R1


Mass: 36075.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060GZX0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na-Cacodylate, 30% 2-methyl-2,4-pentanediol / PH range: 6-7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.66→35.71 Å / Num. obs: 77440 / % possible obs: 99.91 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.07831 / Net I/σ(I): 17.63

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GY0

4gy0


Resolution: 1.66→35.706 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 3995 5.16 %
Rwork0.1794 --
obs0.1815 77419 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→35.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 30 333 5393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165548
X-RAY DIFFRACTIONf_angle_d1.6527581
X-RAY DIFFRACTIONf_dihedral_angle_d14.8692077
X-RAY DIFFRACTIONf_chiral_restr0.079879
X-RAY DIFFRACTIONf_plane_restr0.009994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.67950.30921140.26042526X-RAY DIFFRACTION100
1.6795-1.70.28261090.24922508X-RAY DIFFRACTION100
1.7-1.72150.31971250.24882531X-RAY DIFFRACTION100
1.7215-1.74420.27241440.24522497X-RAY DIFFRACTION100
1.7442-1.76810.29511190.2332498X-RAY DIFFRACTION100
1.7681-1.79330.29341270.23272505X-RAY DIFFRACTION100
1.7933-1.82010.26121170.22632542X-RAY DIFFRACTION100
1.8201-1.84850.24121430.21652497X-RAY DIFFRACTION100
1.8485-1.87880.32121530.21772497X-RAY DIFFRACTION100
1.8788-1.91120.25911450.21822488X-RAY DIFFRACTION100
1.9112-1.9460.24511640.23192504X-RAY DIFFRACTION100
1.946-1.98340.2541460.22142488X-RAY DIFFRACTION100
1.9834-2.02390.26461190.2052541X-RAY DIFFRACTION100
2.0239-2.06790.27791310.2052496X-RAY DIFFRACTION100
2.0679-2.1160.22791530.20552500X-RAY DIFFRACTION100
2.116-2.16890.25251840.19572473X-RAY DIFFRACTION100
2.1689-2.22760.23571210.18832544X-RAY DIFFRACTION100
2.2276-2.29310.25411390.19062506X-RAY DIFFRACTION100
2.2931-2.36710.24371370.18782565X-RAY DIFFRACTION100
2.3671-2.45170.22611120.17932543X-RAY DIFFRACTION100
2.4517-2.54980.22041600.18092499X-RAY DIFFRACTION100
2.5498-2.66580.22631550.1772523X-RAY DIFFRACTION100
2.6658-2.80630.19831530.16922528X-RAY DIFFRACTION100
2.8063-2.98210.22561190.16932545X-RAY DIFFRACTION100
2.9821-3.21220.19871910.16832525X-RAY DIFFRACTION100
3.2122-3.53520.1981290.16322583X-RAY DIFFRACTION100
3.5352-4.04610.1741050.14382628X-RAY DIFFRACTION100
4.0461-5.09530.16641570.13752591X-RAY DIFFRACTION100
5.0953-35.71460.17941240.16152753X-RAY DIFFRACTION100

+
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