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- PDB-1v6y: Crystal Structure Of chimeric Xylanase between Streptomyces Oliva... -

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Basic information

Entry
Database: PDB / ID: 1v6y
TitleCrystal Structure Of chimeric Xylanase between Streptomyces Olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex
ComponentsBeta-xylanase,Exoglucanase/xylanase
KeywordsHYDROLASE / xylanase / TIM-barrel / chimeric enzyme
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process / polysaccharide catabolic process
Similarity search - Function
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 ...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 / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Exoglucanase/xylanase / Beta-xylanase
Similarity search - Component
Biological speciesStreptomyces olivaceoviridis (bacteria)
Cellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKaneko, S. / Ichinose, H. / Fujimoto, Z. / Kuno, A. / Yura, K. / Go, M. / Mizuno, H. / Kusakabe, I. / Kobayashi, H.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure and function of a family 10 beta-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex
Authors: Kaneko, S. / Ichinose, H. / Fujimoto, Z. / Kuno, A. / Yura, K. / Go, M. / Mizuno, H. / Kusakabe, I. / Kobayashi, H.
History
DepositionDec 4, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 10, 2024Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_genus

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-xylanase,Exoglucanase/xylanase


Theoretical massNumber of molelcules
Total (without water)35,9721
Polymers35,9721
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.480, 57.190, 106.670
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 Beta-xylanase,Exoglucanase/xylanase


Mass: 35972.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimeric enzyme from two xylanases,chimeric enzyme from two xylanases
Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria), (gene. exp.) Cellulomonas fimi (bacteria)
Species: , / Plasmid: pET28 / Gene: cex, xynB / Production host: Escherichia coli (E. coli)
References: UniProt: Q7SI98, UniProt: P07986, endo-1,4-beta-xylanase, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Oct 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 13853 / Num. obs: 13853 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.7
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 10.1 / Num. unique all: 1127 / % possible all: 77.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XYF and 2EXO

1xyf

2exo


Resolution: 2.2→28.67 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 108499.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1396 10.2 %RANDOM
Rwork0.153 ---
obs0.153 13714 87.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8769 Å2 / ksol: 0.364045 e/Å3
Displacement parametersBiso mean: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--0.68 Å20 Å2
3---0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 0 240 2697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.216 179 9 %
Rwork0.162 1800 -
obs-1979 78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBO_REP.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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