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- PDB-1hix: CRYSTALLOGRAPHIC ANALYSES OF FAMILY 11 ENDO-BETA-1,4-XYLANASE XYL... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)

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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

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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: 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.

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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

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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

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