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- PDB-1clx: CATALYTIC CORE OF XYLANASE A -

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Basic information

Entry
Database: PDB / ID: 1clx
TitleCATALYTIC CORE OF XYLANASE A
ComponentsXYLANASE A
KeywordsXYLANASE / FAMILY-F XYLANASE FAMILY 10 GLYCOSYL-HYDROLASE
Function / homology
Function and homology information


cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain ...Carbohydrate binding module family 10 / CBM10 superfamily / Cellulose or protein binding domain / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / 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 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsHarris, G.W. / Jenkins, J.A. / Connerton, I. / Pickersgill, R.W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Refined crystal structure of the catalytic domain of xylanase A from Pseudomonas fluorescens at 1.8 A resolution.
Authors: Harris, G.W. / Jenkins, J.A. / Connerton, I. / Pickersgill, R.W.
#1: Journal: FEBS Lett. / Year: 1995
Title: Beta-Glucosidase, Beta-Galactosidase, Family a Cellulases, Family F Xylanases and Two Barley Glycanases Form a Superfamily of Enzymes with 8-Fold Beta/Alpha Architecture and with Two Conserved ...Title: Beta-Glucosidase, Beta-Galactosidase, Family a Cellulases, Family F Xylanases and Two Barley Glycanases Form a Superfamily of Enzymes with 8-Fold Beta/Alpha Architecture and with Two Conserved Glutamates Near the Carboxy-Terminal Ends of Beta-Strands Four and Seven
Authors: Jenkins, J. / Lo Leggio, L. / Harris, G. / Pickersgill, R.
#2: Journal: Structure / Year: 1994
Title: Structure of the Catalytic Core of the Family F Xylanase from Pseudomonas Fluorescens and Identification of the Xylopentaose-Binding Sites
Authors: Harris, G.W. / Jenkins, J.A. / Connerton, I. / Cummings, N. / Lo Leggio, L. / Scott, M. / Hazlewood, G.P. / Laurie, J.I. / Gilbert, H.J. / Pickersgill, R.W.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Analysis of the Catalytic Domain of Xylanase a from Pseudomonas Fluorescens Subspecies Cellulosa
Authors: Pickersgill, R.W. / Jenkins, J.A. / Scott, M. / Connerton, I. / Hazlewood, G.P. / Gilbert, H.J.
History
DepositionAug 31, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XYLANASE A
B: XYLANASE A
C: XYLANASE A
D: XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,0028
Polymers153,8424
Non-polymers1604
Water19,9611108
1
A: XYLANASE A
B: XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0014
Polymers76,9212
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: XYLANASE A
D: XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0014
Polymers76,9212
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.110, 97.320, 151.030
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
XYLANASE A


Mass: 38460.477 Da / Num. of mol.: 4 / Fragment: CATALYTIC CORE, RESIDUES 264 - 611
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Strain: CELLULOSA / Gene: TRUNCATED XYNA (CODONS 264-611 / Plasmid: PET3A / Gene (production host): TRUNCATED XYNA (CODONS 264-611) / Production host: Escherichia coli (E. coli) / References: UniProt: P14768, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1108 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE IS OF THE CATALYTIC CORE OF XYLANASE A; THE COMPLETE XYLANASE WOULD ALSO CONSIST OF A ...THE STRUCTURE IS OF THE CATALYTIC CORE OF XYLANASE A; THE COMPLETE XYLANASE WOULD ALSO CONSIST OF A CELLULOSE BINDING DOMAIN AND A LINKER AS WELL AS THE CATALYTIC BINDING DOMAIN. A TRUNCATED GENE ENCODING THE CARBOXY-TERMINAL DOMAIN (I.E. THE CATALYTIC CORE) WAS EXPRESSED INDEPENDENTLY OF THE CELLULOSE BINDING DOMAIN AND THE LINKER.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
123.3 mg/mlprotein1drop
22.2-2.7 %PEG34001drop
366.7 mMphosphate1drop
410-12 %PEG34001reservoir
5200 mMphosphate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.92
DetectorDetector: IMAGE PLATE / Date: Jan 11, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 105167 / % possible obs: 78.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.077
Reflection
*PLUS
Highest resolution: 1.79 Å / Lowest resolution: 6.92 Å / Num. measured all: 703625
Reflection shell
*PLUS
Highest resolution: 1.79 Å / Lowest resolution: 1.85 Å / % possible obs: 61.5 % / Num. unique obs: 7963 / Num. measured obs: 27549 / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
DENZOdata reduction
RESTRAINrefinement
RefinementResolution: 1.8→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.166 -
obs-103749
Displacement parametersBiso mean: 16.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10800 0 4 1108 11912
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d0.027
X-RAY DIFFRACTIONx_planar_d0.012
X-RAY DIFFRACTIONx_plane_restr0.005
X-RAY DIFFRACTIONx_chiral_restr0.011

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