[English] 日本語
Yorodumi
- PDB-1gok: Thermostable xylanase I from Thermoascus aurantiacus- Crystal form II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gok
TitleThermostable xylanase I from Thermoascus aurantiacus- Crystal form II
ComponentsENDO-1,4-BETA-XYLANASEXylanase
KeywordsHYDROLASE / XYLANASE / FAMILY 10 / PLANT CELL WALL DEGRADATION
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. / Pickersgill, R.W.
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.M. / 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. / Lo Leggio, L. / Pickersgill, R. / Cardin, C.
#2: Journal: Proteins: Struct.,Funct., Genet. / 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: Biochem.Soc.Trans. / Year: 1998
Title: Superfamilies: The 4/7 Superfamily of Beta/ Alpha-Barrel Glycosidases and the Right-Handed Parallel Beta-Helix Superfamily
Authors: Pickersgill, R. / Harris, G. / Lo Leggio, L. / Mayans, O. / Jenkins, J.
#4: Journal: Structural Studies of Xylanases and Endoglucanases / Year: 1997
Title: Structure Solution of Thermoascus Aurantiacus Xylanase. Structural Studies of Xylanases and Endoglucanases
Authors: Lo Leggio, L.
History
DepositionOct 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2001Provider: repository / Type: Initial release
SupersessionJun 18, 2002ID: 1TAX
Revision 1.1Sep 4, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Atomic model / Polymer sequence / Category: atom_site / entity_poly
Item: _atom_site.occupancy / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDO-1,4-BETA-XYLANASE


Theoretical massNumber of molelcules
Total (without water)32,8911
Polymers32,8911
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
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 ENDO-1,4-BETA-XYLANASE / Xylanase / XYLANASE / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE / TAXI


Mass: 32890.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMOASCUS AURANTIACUS (fungus) / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-26 REFER TO THE SIGNAL PEPTIDE. IT IS NOT KNOWN IF GLN 303 IS PRESENT IN THE CRYSTAL

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 32.9 % / Description: THE PH OF CRYSTALLIZATION WAS NOT BUFFERED
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROPS CONTAINING 1:1 RATIO OF 20 MG/ML PROTEIN SOLUTION AND RESERVOIR SOLUTION (12 % TO 25 % PEG 6,000)., pH 7.00

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 1995 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: 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. obs: 80691 / % possible obs: 85.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.82
Reflection shellResolution: 1.14→1.15 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3.15 / % possible all: 78.8

-
Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EXO

2exo


Resolution: 1.14→39.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: A VERY IMPORTANT STEP TOWARDS STRUCTURE SOLUTION WAS REFINEMENT USING ARP (AUTOMATED REFINEMENT PROCEDURE)
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2795 3.5 %FREER FLAG (CCP4)
Rwork0.18 ---
obs0.18 80632 85.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.6 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 13.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.847 Å20 Å2-1.132 Å2
2--0.277 Å20 Å2
3---0.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.1404 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.0939 Å0.0889 Å
Refinement stepCycle: LAST / Resolution: 1.14→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 0 248 2560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.44
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.7142
X-RAY DIFFRACTIONc_mcangle_it1.0862.5
X-RAY DIFFRACTIONc_scbond_it1.3222.5
X-RAY DIFFRACTIONc_scangle_it2.0443
LS refinement shellResolution: 1.14→1.16 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 133 3.79 %
Rwork0.354 3375 -
obs--75.1 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

+
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