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- PDB-1xas: CRYSTAL STRUCTURE, AT 2.6 ANGSTROMS RESOLUTION, OF THE STREPTOMYC... -

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Basic information

Entry
Database: PDB / ID: 1xas
TitleCRYSTAL STRUCTURE, AT 2.6 ANGSTROMS RESOLUTION, OF THE STREPTOMYCES LIVIDANS XYLANASE A, A MEMBER OF THE F FAMILY OF BETA-1,4-D-GLYCANSES
Components1,4-BETA-D-XYLAN XYLANOHYDROLASE
KeywordsXYLANASE A
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / extracellular region
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 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. ...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 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsDerewenda, U. / Derewenda, Z.S.
CitationJournal: J.Biol.Chem. / Year: 1994
Title: Crystal structure, at 2.6-A resolution, of the Streptomyces lividans xylanase A, a member of the F family of beta-1,4-D-glycanases.
Authors: Derewenda, U. / Swenson, L. / Green, R. / Wei, Y. / Morosoli, R. / Shareck, F. / Kluepfel, D. / Derewenda, Z.S.
History
DepositionMay 31, 1994Processing site: BNL
Revision 1.0May 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,4-BETA-D-XYLAN XYLANOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)32,9711
Polymers32,9711
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.520, 46.510, 85.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 1,4-BETA-D-XYLAN XYLANOHYDROLASE / Coordinate model: Cα atoms only


Mass: 32971.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / References: UniProt: P26514, endo-1,4-beta-xylanase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 mg/mlprotein1drop
25 %PEG40001drop
3100 mMsodium acetate1drop
45 %PEG40001reservoir
5100 mMsodium acetate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.59 Å / Lowest resolution: 100 Å / Num. obs: 8479 / % possible obs: 92.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
Highest resolution: 2.59 Å / Lowest resolution: 2.75 Å / % possible obs: 56.1 % / Mean I/σ(I) obs: 9.08

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→10 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.21 -
obs0.21 8008
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms295 0 0 0 295
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.3791
X-RAY DIFFRACTIONx_mcangle_it0.6361.5
X-RAY DIFFRACTIONx_scbond_it0.6791.5
X-RAY DIFFRACTIONx_scangle_it1.0772
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.045
X-RAY DIFFRACTIONx_planar_d0.050.048
X-RAY DIFFRACTIONx_plane_restr0.020.012
X-RAY DIFFRACTIONx_chiral_restr0.10.095

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