[English] 日本語
Yorodumi
- PDB-4ou4: Crystal structure of esterase rPPE mutant S159A complexed with (S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ou4
TitleCrystal structure of esterase rPPE mutant S159A complexed with (S)-Ac-CPA
ComponentsAlpha/beta hydrolase fold-3 domain protein
KeywordsHYDROLASE / A/B HYDROLASE FOLD / ESterase / HSL-like family
Function / homology
Function and homology information


Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-(acetyloxy)(2-chlorophenyl)ethanoic acid / Alpha/beta hydrolase fold-3 domain protein
Similarity search - Component
Biological speciesPseudomonas (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDou, S. / Kong, X.D. / Ma, B.D. / Xu, J.H. / Zhou, J.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structures of Pseudomonas putida esterase reveal the functional role of residues 187 and 287 in substrate binding and chiral recognition
Authors: Dou, S. / Kong, X.D. / Ma, B.D. / Chen, Q. / Zhang, J. / Zhou, J.H. / Xu, J.H.
History
DepositionFeb 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 8, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha/beta hydrolase fold-3 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7612
Polymers36,5321
Non-polymers2291
Water1,76598
1
A: Alpha/beta hydrolase fold-3 domain protein
hetero molecules

A: Alpha/beta hydrolase fold-3 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5224
Polymers73,0652
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)94.624, 94.624, 88.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

21A-585-

HOH

31A-590-

HOH

41A-595-

HOH

-
Components

#1: Protein Alpha/beta hydrolase fold-3 domain protein / Esterase


Mass: 36532.320 Da / Num. of mol.: 1 / Mutation: S159A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (bacteria) / Strain: ECU1011 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L7PYQ2, carboxylesterase
#2: Chemical ChemComp-S2T / (2S)-(acetyloxy)(2-chlorophenyl)ethanoic acid


Mass: 228.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9ClO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THE SEQUENCE DATABASE WAS WRONG AT THIS POSITION. RESIDUE 10 SHOULD BE GLN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16% (w/v) PEG8000, 0.04M KH2PO4, 20% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 13, 2013
RadiationMonochromator: VARIMAX-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16307 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 33.19 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.498.70.81100
2.49-2.598.70.6721100
2.59-2.78.80.5651100
2.7-2.858.80.4551100
2.85-3.028.70.3431100
3.02-3.268.80.2461100
3.26-3.588.70.1711100
3.58-4.18.70.1151100
4.1-5.178.60.077199.9
5.17-5080.07199.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YH2
Resolution: 2.4→42.317 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 819 5.04 %
Rwork0.1672 --
obs0.1704 16258 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.49 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 15 98 2539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082518
X-RAY DIFFRACTIONf_angle_d1.1223426
X-RAY DIFFRACTIONf_dihedral_angle_d14.064907
X-RAY DIFFRACTIONf_chiral_restr0.042380
X-RAY DIFFRACTIONf_plane_restr0.006449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.399-2.54930.26191480.1873248999
2.5493-2.74610.2561280.17962512100
2.7461-3.02240.27431480.17612537100
3.0224-3.45950.22831440.16292545100
3.4595-4.3580.21451270.15932598100
4.358-42.32370.22031240.1642758100

+
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