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- PDB-1xyz: A COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN TWO DISTINCT FAM... -

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Basic information

Entry
Database: PDB / ID: 1xyz
TitleA COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN TWO DISTINCT FAMILIES OF BETA-GLYCANASES
Components1,4-BETA-D-XYLAN-XYLANOHYDROLASE
KeywordsGLYCOSYLTRANSFERASE / GLYCOSYL HYDROLASE / XYLANASE / FAMILY F/10 OF GLYCOSYL HYDROLASES / CLOSTRIDIUM THERMOCELLUM
Function / homology
Function and homology information


xylan endo-1,3-beta-xylosidase activity / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding
Similarity search - Function
Cellulose binding, type IV / Cellulose Binding Domain Type IV / Esterase-like / Putative esterase / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. ...Cellulose binding, type IV / Cellulose Binding Domain Type IV / Esterase-like / Putative esterase / Carbohydrate binding module (family 6) / Clostridium cellulosome enzymes repeated domain signature. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycosidases / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase Z
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsAlzari, P.M. / Spinelli, S. / Dominguez, R.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: A common protein fold and similar active site in two distinct families of beta-glycanases.
Authors: Dominguez, R. / Souchon, H. / Spinelli, S. / Dauter, Z. / Wilson, K.S. / Chauvaux, S. / Beguin, P. / Alzari, P.M.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary Diffraction Analysis of the Catalytic Domain of Xylanase Z from Clostridium Thermocellum
Authors: Souchon, H. / Spinelli, S. / Beguin, P. / Alzari, P.M.
History
DepositionJun 7, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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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
B: 1,4-BETA-D-XYLAN-XYLANOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)78,8682
Polymers78,8682
Non-polymers00
Water8,233457
1
A: 1,4-BETA-D-XYLAN-XYLANOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)39,4341
Polymers39,4341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1,4-BETA-D-XYLAN-XYLANOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)39,4341
Polymers39,4341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.100, 51.100, 70.740
Angle α, β, γ (deg.)100.54, 83.79, 101.64
Int Tables number1
Space group name H-MP1
Atom site foot note1: HIS A 596 - THR A 597 OMEGA = 0.11 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: HIS B 596 - THR B 597 OMEGA = 0.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99997, 0.00357, 0.00622), (0.00634, 0.03409, 0.9994), (0.00336, 0.99941, -0.03411)
Vector: 23.67979, -4.45463, 56.27028)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 516 .. A 835 B 516 .. B 835 0.287

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Components

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


Mass: 39434.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: NCIB 10682 / Plasmid: PCT1214 (PUC8) / Production host: Escherichia coli (E. coli) / References: UniProt: P10478, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMTris-HCl1drop
320 %PEG20001reservoir
40.2 Mcalcium acetate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 11704 / % possible obs: 96.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.083
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 10 Å / Num. obs: 117046 / Num. measured all: 343930 / Rmerge(I) obs: 0.083

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Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.4→10 Å / σ(F): 0
RfactorNum. reflection
Rfree0.221 -
Rwork0.183 -
obs0.183 117046
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5166 0 0 457 5623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.58
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.58

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