[English] 日本語
Yorodumi
- PDB-6z68: A novel metagenomic alpha/beta-fold esterase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z68
TitleA novel metagenomic alpha/beta-fold esterase
ComponentsAcetyl esterase/lipase
KeywordsHYDROLASE / alpha/beta-fold hydrolase / esterase / metagenome / inhibitor-bound / substrate promiscuity
Function / homology: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / DI(HYDROXYETHYL)ETHER / Acetyl esterase/lipase
Function and homology information
Biological speciesPseudonocardia thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBollinger, A. / Thies, S. / Hoeppner, A. / Kobus, S. / Jaeger, K.-E. / Smits, S.H.J.
CitationJournal: Febs J. / Year: 2021
Title: Crystal structures of a novel family IV esterase in free and substrate-bound form.
Authors: Hoppner, A. / Bollinger, A. / Kobus, S. / Thies, S. / Coscolin, C. / Ferrer, M. / Jaeger, K.E. / Smits, S.H.J.
History
DepositionMay 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl esterase/lipase
B: Acetyl esterase/lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6527
Polymers81,0272
Non-polymers6255
Water16,862936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint6 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.710, 77.190, 162.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein Acetyl esterase/lipase


Mass: 40513.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia thermophila (bacteria) / Gene: SAMN05443637_118146 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M6Y2K1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 936 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.25 M magnesium chloride, 0.1 M Tris pH 8.5 and 35 % (w/v) PEG 4000 with 0.01 M TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976246 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976246 Å / Relative weight: 1
ReflectionResolution: 1.35→55.28 Å / Num. obs: 155980 / % possible obs: 96.69 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.64
Reflection shellResolution: 1.353→1.402 Å / Rmerge(I) obs: 0.488 / Num. unique obs: 10966 / CC1/2: 0.804

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
Auto-Rickshawphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: xxxx

Resolution: 1.35→55.28 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.086 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1841 1994 1.3 %RANDOM
Rwork0.1376 ---
obs0.1381 153608 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.09 Å2 / Biso mean: 18.011 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å20 Å20 Å2
2--1.85 Å20 Å2
3---1.13 Å2
Refinement stepCycle: final / Resolution: 1.35→55.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5428 0 41 936 6405
Biso mean--41.14 34.47 -
Num. residues----720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0135702
X-RAY DIFFRACTIONr_bond_other_d0.0050.0175307
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.6497776
X-RAY DIFFRACTIONr_angle_other_deg1.6171.57112254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.620.095316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67315837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8581559
X-RAY DIFFRACTIONr_chiral_restr0.1160.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026577
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021252
X-RAY DIFFRACTIONr_rigid_bond_restr7.916311009
LS refinement shellResolution: 1.353→1.388 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 88 -
Rwork0.3 6671 -
all-6759 -
obs--57.39 %

+
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