[English] 日本語
Yorodumi
- PDB-1k6a: Structural studies on the mobility in the active site of the Ther... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k6a
TitleStructural studies on the mobility in the active site of the Thermoascus aurantiacus xylanase I
Componentsxylanase I
KeywordsHYDROLASE / alternate conformations / active site mobility
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsLo Leggio, L. / Kalogiannis, S. / Eckert, K. / Teixeira, S.C.M. / Bhat, M.K. / Andrei, C. / Pickersgill, R.W. / Larsen, S.
Citation
Journal: FEBS LETT. / Year: 2001
Title: Substrate specificity and subsite mobility in T. aurantiacus xylanase 10A.
Authors: Lo Leggio, L. / Kalogiannis, S. / Eckert, K. / Teixeira, S.C. / Bhat, M.K. / Andrei, C. / Pickersgill, R.W. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Anisotropic refinement of the structure of Thermoascus aurantiacus xylanase I
Authors: Teixeira, S.C.M. / Lo Leggio, L. / Pickersgill, R. / Cardin, C.
#2: Journal: Proteins / Year: 1999
Title: High Resolution Structure and Sequence of T.aurantiacus Xylanase I: Implications for the Evolution of thermostability in Family 10 xylanases and enzymes with (beta)alpha-barrel architecture
Authors: Lo Leggio, L. / Kalogiannis, S. / Bhat, M.K. / Pickersgill, R.W.
#3: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure at 1.8A resolution and proposed amino acid sequence of a thermostable xylanase from Thermoascus aurantiacus
Authors: Natesh, R. / Bhanumoorthy, P. / Vithayathil, P.J. / Sekar, K. / Ramakumar, S. / Viswamitra, M.A.
History
DepositionOct 15, 2001Deposition site: RCSB / Processing site: PDBJ
SupersessionJul 3, 2002ID: 1FXM
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: xylanase I


Theoretical massNumber of molelcules
Total (without water)32,9081
Polymers32,9081
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.220, 59.240, 51.310
Angle α, β, γ (deg.)90.00, 109.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein xylanase I / / Endo-1 / 4-beta-xylanase


Mass: 32907.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermoascus aurantiacus (fungus) / Strain: IMI 216529 / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.6338.73
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop5.1PEG 6K, phosphate citrate buffer, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop7.8PEG 6K, EDTA, Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX9.610.87
SYNCHROTRONSRS PX9.620.87
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.14→39.5 Å / Num. all: 80691 / Num. obs: 80508 / % possible obs: 85.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.14→1.15 Å / % possible all: 72.7

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→10 Å / Num. parameters: 23110 / Num. restraintsaints: 29211 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1458 4019 5.3 %RANDOM
Rwork0.1093 ---
all0.11 76489 --
obs0.1065 80628 80.9 %-
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 2089 / Occupancy sum non hydrogen: 2518.01
Refinement stepCycle: LAST / Resolution: 1.14→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 0 199 4740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.091
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.042
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.054
LS refinement shellResolution: 1.14→1.15 Å /
Rfactor% reflection
Rwork0.097 -
obs-79.9 %

+
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