[English] 日本語
Yorodumi
- PDB-4hhq: Serum paraoxonase-1 by directed evolution with the H115Q and H134... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hhq
TitleSerum paraoxonase-1 by directed evolution with the H115Q and H134Q mutations
ComponentsSERUM PARAOXONASE BY DIRECTED EVOLUTION
KeywordsHYDROLASE / 6-blades -propeller fold
Function / homologyTolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / BROMIDE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoshe, B.-D. / Grzegorz, W. / Mikael, E. / Israel, S. / Joel, L.S. / Dan, S.T.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme.
Authors: Ben-David, M. / Wieczorek, G. / Elias, M. / Silman, I. / Sussman, J.L. / Tawfik, D.S.
History
DepositionOct 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERUM PARAOXONASE BY DIRECTED EVOLUTION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4147
Polymers39,5841
Non-polymers8306
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.789, 93.789, 144.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein SERUM PARAOXONASE BY DIRECTED EVOLUTION


Mass: 39583.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Gene: Homo sapiens, oryctolagus cuniculus, mus musculus, rattus rattus
Plasmid details: FROM SHUFFLED GENES OF HOMO SAPIENS, ORYCTOLAGUS CUNICULUS, MUS MUSCULUS, AND RATTUS
Plasmid: PET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami DE3
References: arylesterase, aryldialkylphosphatase, 1,4-lactonase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALLIZED SEQUENCE REPRESENTS A CHIMERIC CONSTRUCT OF PARAOXONASE-1 FROM FOUR DIFFERENCE SOURCES

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.2M NaBr, 0.1M Bis-tris propane , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→39.34 Å / Num. all: 27832 / Num. obs: 27832 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 30.187 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.086 / Net I/σ(I): 30.93
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2860 / Rsym value: 0.519 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0111refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.34 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.66 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 1491 5.1 %RANDOM
Rwork0.1766 ---
all0.17871 27832 --
obs0.17871 27832 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.187 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 29 147 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222615
X-RAY DIFFRACTIONr_angle_refined_deg2.1911.9633576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3855323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24125.043117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75915401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6157
X-RAY DIFFRACTIONr_chiral_restr0.1710.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211981
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 101 -
Rwork0.231 1832 -
obs--99.95 %

+
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