[English] 日本語
Yorodumi
- PDB-6sz0: The glucuronoyl esterase OtCE15A H408A variant from Opitutus terrae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sz0
TitleThe glucuronoyl esterase OtCE15A H408A variant from Opitutus terrae
Componentsglucuronoyl esterase OtCE15A
KeywordsHYDROLASE / Esterase / Complex / Biomass
Function / homologyGlucuronyl esterase, fungi / Alpha/Beta hydrolase fold / metal ion binding / DI(HYDROXYETHYL)ETHER / Putative acetyl xylan esterase
Function and homology information
Biological speciesOpitutus terrae PB90-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMazurkewich, S. / Navarro Poulsen, J.C. / Larsbrink, J. / Lo Leggio, L.
Funding support Sweden, Denmark, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Novo Nordisk FoundationNNF17OC0027698 Denmark
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural and biochemical studies of the glucuronoyl esteraseOtCE15A illuminate its interaction with lignocellulosic components.
Authors: Mazurkewich, S. / Poulsen, J.N. / Lo Leggio, L. / Larsbrink, J.
History
DepositionOct 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: glucuronoyl esterase OtCE15A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6559
Polymers46,0811
Non-polymers5738
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-17 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.197, 44.204, 50.154
Angle α, β, γ (deg.)76.310, 65.696, 70.744
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein glucuronoyl esterase OtCE15A


Mass: 46081.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opitutus terrae PB90-1 (bacteria) / Gene: Oter_0116 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1ZMF4

-
Non-polymers , 6 types, 231 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution C12: 0.09 M NPS (0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate), 0.1 M Buffer System ...Details: Enzyme mixed 50/50 with reservoir solution containing Morpheus screen solution C12: 0.09 M NPS (0.3M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3M Ammonium sulfate), 0.1 M Buffer System 3 pH 8.5 (Tris; BICINE), 50 % v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.738→45.39 Å / Num. obs: 30758 / % possible obs: 94.21 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04631 / Rpim(I) all: 0.0293 / Rrim(I) all: 0.055 / Net I/σ(I): 14.6
Reflection shellResolution: 1.738→1.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3377 / Mean I/σ(I) obs: 2.85 / Num. unique obs: 2499 / CC1/2: 0.945 / Rpim(I) all: 0.2129 / Rrim(I) all: 0.4005 / % possible all: 76.75

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gs0

6gs0


Resolution: 1.74→45.39 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 24.1081
RfactorNum. reflection% reflection
Rfree0.1921 2306 7.5 %
Rwork0.1423 --
obs0.1459 30727 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.06 Å2
Refinement stepCycle: LAST / Resolution: 1.74→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 35 223 3321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893264
X-RAY DIFFRACTIONf_angle_d1.00574457
X-RAY DIFFRACTIONf_chiral_restr0.0573466
X-RAY DIFFRACTIONf_plane_restr0.0071597
X-RAY DIFFRACTIONf_dihedral_angle_d17.5751190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.34561000.32111238X-RAY DIFFRACTION66.3
1.78-1.820.28051450.22131785X-RAY DIFFRACTION93.73
1.82-1.860.26231450.2011785X-RAY DIFFRACTION95.31
1.86-1.910.27911450.18921786X-RAY DIFFRACTION94.56
1.91-1.970.25411450.17431788X-RAY DIFFRACTION94.62
1.97-2.030.22011460.16621798X-RAY DIFFRACTION95.11
2.03-2.110.20461450.15521789X-RAY DIFFRACTION95.46
2.11-2.190.25471450.13791796X-RAY DIFFRACTION95.05
2.19-2.290.17841470.13651805X-RAY DIFFRACTION95.64
2.29-2.410.1971470.13671812X-RAY DIFFRACTION96.17
2.41-2.560.19791490.13221838X-RAY DIFFRACTION96.69
2.56-2.760.15891490.12931826X-RAY DIFFRACTION97.05
2.76-3.040.17251480.1321828X-RAY DIFFRACTION97.73
3.04-3.480.17481490.12641843X-RAY DIFFRACTION98.03
3.48-4.380.15831510.11421859X-RAY DIFFRACTION97.76
4.38-45.390.18631500.14981845X-RAY DIFFRACTION97.99

+
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