[English] 日本語
Yorodumi
- PDB-1g66: ACETYLXYLAN ESTERASE AT 0.90 ANGSTROM RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g66
TitleACETYLXYLAN ESTERASE AT 0.90 ANGSTROM RESOLUTION
ComponentsACETYL XYLAN ESTERASE II
KeywordsHYDROLASE / serine hydrolase / acetyl xylopyranose / xylan
Function / homology
Function and homology information


acetylxylan esterase / acetylxylan esterase activity / xylan catabolic process / cellulose catabolic process / extracellular region
Similarity search - Function
Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylxylan esterase 2
Similarity search - Component
Biological speciesPenicillium purpurogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.9 Å
AuthorsGhosh, D. / Sawicki, M. / Lala, P. / Erman, M. / Pangborn, W. / Eyzaguirre, J. / Gutierrez, R. / Jornvall, H. / Thiel, D.J.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Multiple conformations of catalytic serine and histidine in acetylxylan esterase at 0.90 A.
Authors: Ghosh, D. / Sawicki, M. / Lala, P. / Erman, M. / Pangborn, W. / Eyzaguirre, J. / Gutierrez, R. / Jornvall, H. / Thiel, D.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Determination of a protein structure by iodination: the structure of iodinated acetylxylan esterase
Authors: Ghosh, D. / Erman, M. / Sawicki, M. / Lala, P. / Weeks, D.R. / Li, N. / Pangborn, W. / Thiel, D.J. / Jornvall, H. / Gutierrez, R. / Eyzaguirre, J.
#2: Journal: Proteins / Year: 1996
Title: Characterization of crystals of P. purpurogenum acetyl xylan esterase from high resolution X-ray diffraction
History
DepositionNov 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ACETYL XYLAN ESTERASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4149
Polymers20,6621
Non-polymers7538
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.541, 59.898, 71.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ACETYL XYLAN ESTERASE II


Mass: 20661.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium purpurogenum (fungus) / References: UniProt: O59893, acetylesterase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.3
Details: Ammonium sulfate, pH 5.3, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Pangborn, W., (1996) Proteons Struct.Funct.Genet., 24, 523.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
250 mMcitrate1drop
313 %satammonium sulfate1drop
433-37 %satammonium sulfate1reservoir
550 mMcitrate1reservoir

-
Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: PRINCETON 2K / Detector: CCD / Date: Dec 15, 1995
RadiationMonochromator: Sagitally focussed Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 0.9→99 Å / Num. all: 95283 / Num. obs: 95283 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.41 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.2
Reflection shellResolution: 0.9→0.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.185 / % possible all: 40.4
Reflection
*PLUS
Num. measured all: 420882
Reflection shell
*PLUS
% possible obs: 40.4 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.9→99 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.132 4800 RANDOM
Rwork0.107 --
all0.107 95283 -
obs0.107 95283 -
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 0.9→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 44 299 1785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d1.982
X-RAY DIFFRACTIONs_from_restr_planes1.717
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.103
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg25.23
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.717

+
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