[English] 日本語
Yorodumi
- PDB-1hix: CRYSTALLOGRAPHIC ANALYSES OF FAMILY 11 ENDO-BETA-1,4-XYLANASE XYL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hix
TitleCRYSTALLOGRAPHIC ANALYSES OF FAMILY 11 ENDO-BETA-1,4-XYLANASE XYL1 FROM STREPTOMYCES SP. S38
ComponentsENDO-1,4-BETA-XYLANASE
KeywordsHYDROLASE / XYLAN DEGRADATION
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesSTREPTOMYCES SP. S38 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWouters, J. / Georis, J. / Dusart, J. / Frere, J.M. / Depiereux, E. / Charlier, P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallographic Analysis of Family 11 Endo-[Beta]-1,4-Xylanase Xyl1 from Streptomyces Sp. S38
Authors: Wouters, J. / Georis, J. / Engher, D. / Vandenhaute, J. / Dusart, J. / Frere, J.M. / Depiereux, E. / Charlier, P.
#1: Journal: Protein Sci. / Year: 2000
Title: An Additional Aromatic Interaction Improves the Thermostability and Thermophilicity of a Mesophilic Family 11 Endo-B-1,4-Xylanase: Structural Basis and Molecular Study
Authors: Georis, J. / De Lemos Esteves, F. / Lamotte-Brasseur, J. / Bougnet, V. / Devreese, B. / Giannotta, F. / Granier, B. / Frere, J.M.
#2: Journal: Gene / Year: 1999
Title: Sequence, Overproduction and Purification of the Family 11 Endo-B-1,4-Xylanase Encoded by the Xyl1 Gene of Streptomyces Sp. S38
Authors: Georis, J. / Giannotta, F. / Lamotte-Brasseur, J. / Devreese, B. / Van Beeumen, J. / Granier, B. / Frere, J.-M.
History
DepositionJan 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,1942
Polymers41,1942
Non-polymers00
Water3,945219
1
A: ENDO-1,4-BETA-XYLANASE

A: ENDO-1,4-BETA-XYLANASE

A: ENDO-1,4-BETA-XYLANASE


Theoretical massNumber of molelcules
Total (without water)61,7923
Polymers61,7923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
MethodPQS
2
B: ENDO-1,4-BETA-XYLANASE

B: ENDO-1,4-BETA-XYLANASE

B: ENDO-1,4-BETA-XYLANASE


Theoretical massNumber of molelcules
Total (without water)61,7923
Polymers61,7923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.493, 71.493, 130.298
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.44268, -0.89584, 0.03881), (-0.89578, 0.44376, 0.02556), (-0.04012, -0.02346, -0.99892)
Vector: 32.44958, 61.62354, 66.78052)

-
Components

#1: Protein ENDO-1,4-BETA-XYLANASE


Mass: 20597.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES SP. S38 (bacteria)
Description: STREPTOMYCES SP. S38 WAS ISOLATED BY BIO-ARGOS FROM FOREST SOIL (LIEGE, BELGIUM)
Gene: XYL1 / Production host: STREPTOMYCES LIVIDANS (bacteria) / References: UniProt: Q59962, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.962 Å3/Da / Density % sol: 35 %
Crystal growpH: 9 / Details: pH 9.00
Crystal grow
*PLUS
Method: other / Details: Sunna, A., (1997) Crit. Rev. Biotechnol., 17, 39.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.94
DetectorDetector: IMAGE PLATE / Date: Feb 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 22651 / % possible obs: 82.5 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.082 / Rsym value: 0.185 / Net I/σ(I): 5.66
Reflection shellResolution: 2→2.3 Å / Mean I/σ(I) obs: 3.23 / Rsym value: 0.236 / % possible all: 85
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 22088 / Num. measured all: 177572
Reflection shell
*PLUS
% possible obs: 84.96 % / Rmerge(I) obs: 0.236

-
Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BCX

1bcx


Resolution: 2→7 Å / Num. parameters: 12311 / Num. restraintsaints: 15648 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH AND HUBER
Details: ZERO OCCUPANCY FOR LATERAL CHAIN OF RESIDUE TYR 179 IN BOTH SUBUNITS HALF OCCUPANCY FOR 14 WATER MOLECULES ALTERNATE CONFORMATIONS GIVEN FOR THE LATERAL CHAINS OF RESIDUES THR B 9, SER B 18 B 18 AND SER B 40.
RfactorNum. reflection% reflectionSelection details
Rfree0.3087 -5 %EVERY 10TH REFLECTION
obs0.2038 -82.5 %-
all-22088 --
Refine analyzeNum. disordered residues: 3
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 0 219 3073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0.057
X-RAY DIFFRACTIONs_from_restr_planes0.355
X-RAY DIFFRACTIONs_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 16838 / σ(I): 4 / Num. reflection Rfree: 563 / Rfactor all: 0.2038 / Rfactor obs: 0.1846 / Rfactor Rfree: 0.2693 / Rfactor Rwork: 0.1846
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.355
X-RAY DIFFRACTIONs_chiral_restr0.031

+
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