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- PDB-1xys: CATALYTIC CORE OF XYLANASE A E246C MUTANT -

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Basic information

Entry
Database: PDB / ID: 1xys
TitleCATALYTIC CORE OF XYLANASE A E246C MUTANT
ComponentsXYLANASE A
KeywordsHYDROLASE / FAMILY F XYLANASE / FAMILY 10 OF 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. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHarris, G.W. / Jenkins, J.A. / Connerton, I. / Pickersgill, R.W.
Citation
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.
#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: 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
DepositionSep 2, 1994Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,9494
Polymers76,8692
Non-polymers802
Water00
1
A: XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4752
Polymers38,4351
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4752
Polymers38,4351
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.500, 97.500, 152.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9971, 0.0589, 0.0475), (0.0576, 0.1842, 0.9812), (0.049, 0.9811, -0.187)
Vector: 148.60699, -44.492, 44.841)
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 1 .. 345 1 .. 345

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Components

#1: Protein XYLANASE A / Coordinate model: Cα atoms only


Mass: 38434.508 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Ca
Compound detailsCOMPND MOLECULE: XYLANASE A. CATALYTIC DOMAIN.
Nonpolymer detailsCALCIUM 348 IS BOUND TO ASP 256, ASN 261, ASN 253, AND ASN 258.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal
*PLUS
Density % sol: 47 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.1 Msodium cacodylate1reservoir
3200 mMcalcium acetate1reservoir
41 mM2-mercaptoethanol1reservoir
514-18 %(w/v)PEG80001reservoir

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Data collection

DetectorDate: Dec 27, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 25370 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.078

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Processing

Software
NameClassification
RESTRAINrefinement
DENZOdata reduction
RefinementResolution: 2.5→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.2 24996
Displacement parametersBiso mean: 14.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms690 0 2 0 692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.014
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.011
X-RAY DIFFRACTIONp_chiral_restr0.019
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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