[English] 日本語
Yorodumi
- PDB-1bs9: ACETYLXYLAN ESTERASE FROM P. PURPUROGENUM REFINED AT 1.10 ANGSTROMS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bs9
TitleACETYLXYLAN ESTERASE FROM P. PURPUROGENUM REFINED AT 1.10 ANGSTROMS
ComponentsACETYL XYLAN ESTERASE
KeywordsSERINE HYDROLASE / ESTERASE / ALPHA/BETA HYDROLASE
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 / SIRAS / Resolution: 1.1 Å
AuthorsGhosh, D. / Erman, M. / Sawicki, M.W. / Lala, P. / Weeks, D.R. / Li, N. / Pangborn, W. / Thiel, D.J. / Jornvall, H. / Eyzaguirre, J.
CitationJournal: 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.
History
DepositionSep 1, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACETYL XYLAN ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7582
Polymers20,6621
Non-polymers961
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.886, 60.983, 72.425
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


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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.57 Å3/Da / Density % sol: 22 %
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.3 / 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: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.92
DetectorType: PRINCETON 2K / Detector: CCD / Date: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.1→99 Å / Num. obs: 44040 / % possible obs: 69.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 32
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4 / % possible all: 45
Reflection
*PLUS
Num. measured all: 149250
Reflection shell
*PLUS
% possible obs: 44.9 %

-
Processing

Software
NameClassification
DENZOdata reduction
SHELXmodel building
SHELXrefinement
SHELXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.1→99 Å / Num. parameters: 14389 / Num. restraintsaints: 16950 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 2232 5.1 %RANDOM
all0.1226 43972 --
obs0.1279 -69.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 1203 / Occupancy sum non hydrogen: 1576.5
Refinement stepCycle: LAST / Resolution: 1.1→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 5 143 1598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.063
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 44020 / Rfactor Rwork: 0.1279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg25.978
X-RAY DIFFRACTIONs_plane_restr1.465

+
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