[English] 日本語
Yorodumi
- PDB-4zi5: Crystal Structure of Dienelactone Hydrolase-like Promiscuous Phos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zi5
TitleCrystal Structure of Dienelactone Hydrolase-like Promiscuous Phospotriesterase P91 from Metagenomic Libraries
ComponentsP91
KeywordsHYDROLASE / Metagenomic Libraries / alpha/beta Hydrolase / Promiscuity / Phosphotriesterase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsColin, P.-Y. / Fischer, G. / Hyvonen, M. / Hollfelder, F.
CitationJournal: Nat Commun / Year: 2015
Title: Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics.
Authors: Colin, P.Y. / Kintses, B. / Gielen, F. / Miton, C.M. / Fischer, G. / Mohamed, M.F. / Hyvonen, M. / Morgavi, D.P. / Janssen, D.B. / Hollfelder, F.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P91
B: P91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8185
Polymers53,7342
Non-polymers843
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-8 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.613, 73.414, 113.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: -1 - 237 / Label seq-ID: 12 - 250

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein P91


Mass: 26867.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Plasmid: pASKIBA5+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: aryldialkylphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.56 % / Description: shard-like plates
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH=8.5, 0.2M MgCl2, 20% PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91882 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91882 Å / Relative weight: 1
ReflectionResolution: 1.702→61.57 Å / Num. obs: 45156 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 12.5
Reflection shellResolution: 1.702→1.708 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2 / Rsym value: 0.454 / % possible all: 55.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDS(VERSION January 10data reduction
Aimless(version 0.3.8)data scaling
PHASERphasing
autoPROCdata reduction
CCP46.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F67

3f67


Resolution: 1.702→61.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.654 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20744 2180 4.8 %RANDOM
Rwork0.18263 ---
obs0.18385 42939 87.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.248 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0 Å2
2--0.26 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.702→61.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 3 456 4045
Refine LS restraints NCS

Ens-ID: 1 / Number: 28118 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 137 -
Rwork0.318 2650 -
obs--73.83 %

+
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