[English] 日本語
Yorodumi
- PDB-1i1x: 1.11 A ATOMIC RESOLUTION STRUCTURE OF A THERMOSTABLE XYLANASE FRO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i1x
Title1.11 A ATOMIC RESOLUTION STRUCTURE OF A THERMOSTABLE XYLANASE FROM THERMOASCUS AURANTIACUS
ComponentsENDO-1,4-BETA-XYLANASE
KeywordsHYDROLASE / XYLAN DEGRADATION / GLYCOSIDASE / ENZYME / ATOMIC RESOLUTION / ROOM TEMPERATURE / 1 / 4-BETA-XYLAN XYLANOHYDROLASE
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. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / 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. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / 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: 1.11 Å
AuthorsNatesh, R. / Ramakumar, S. / Viswamitra, M.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 A) at 100 K and atomic resolution (1.11 A) at 293 K refined anisotropically to small-molecule accuracy.
Authors: Natesh, R. / Manikandan, K. / Bhanumoorthy, P. / Viswamitra, M.A. / Ramakumar, S.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure at 1.8 A Resolution and Proposed Amino Acid Sequence of a Thermostable Xylanase from Thermoascus Aurantiascus
Authors: Natesh, R. / Bhanumoorthy, P. / Vithayathil, P.J. / Sekar, K. / Ramakumar, S. / Viswamitra, M.A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Crystals of Thermoascus Aurantiacus Xylanase
Authors: Viswamitra, M.A. / Bhanumoorthy, P. / Ramakumar, S. / Manjula, M.V. / Vithayathil, P.J. / Murthy, S.K. / Naren, A.P.
History
DepositionFeb 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 9, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,8691
Polymers32,8691
Non-polymers00
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.520, 68.090, 51.440
Angle α, β, γ (deg.)90.00, 113.56, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ENDO-1,4-BETA-XYLANASE / XYLANASE / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE


Mass: 32868.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermoascus aurantiacus (fungus) / Strain: STRAIN ISOLATED FROM LOCAL INDIAN SOIL / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: CRYSTALS WERE GROWN BY SITTING DROP AGAINST 12% AMMONIUM SULPHATE SOLUTION AT THE SAME BUFFER CONDITION IN THE RESERVOIR., pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Viswamitra, M.A., (1993) J.Mol.Biol., 232, 987.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %protein1drop
210 %(w/v)PEG60001drop
350 %PEG60001reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.009 / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 1999 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.11→25 Å / Num. obs: 90855 / % possible obs: 87.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.6
Reflection shellResolution: 1.11→1.15 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 81.3
Reflection
*PLUS
Redundancy: 3.25 % / Num. measured all: 294946
Reflection shell
*PLUS
% possible obs: 81.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.98

-
Processing

Software
NameVersionClassification
HKL-2000SUITEdata collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TUX (1.8 A)

1tux


Resolution: 1.11→10 Å / Num. parameters: 22784 / Num. restraintsaints: 28345 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: CNS 0.4 was also used for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.1236 1745 2 %RANDOM
Rwork0.0994 ---
all-85628 --
obs-85628 82.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 29 / Occupancy sum hydrogen: 2119.2 / Occupancy sum non hydrogen: 2536.06
Refinement stepCycle: LAST / Resolution: 1.11→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4509 0 0 267 4776
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0286
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.1
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.1
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg24.3
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.73

+
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