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- PDB-1xwt: Structure Of A Cold-Adapted Family 8 Xylanase -

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Basic information

Entry
Database: PDB / ID: 1xwt
TitleStructure Of A Cold-Adapted Family 8 Xylanase
Componentsendo-1,4-beta-xylanase
KeywordsHYDROLASE / XYLAN DEGRADATION / PSYCHROPHILIC / COLD ADAPTATION / TEMPERATURE / GLYCOSYL HYDROLASE / FAMILY 8
Function / homology
Function and homology information


cellulase / cellulase activity / xylan catabolic process / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 8 / Glycosyl hydrolases family 8 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudoalteromonas haloplanktis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDe Vos, D. / Collins, T. / Hoyoux, A. / Savvides, S.N. / Gerday, C. / Van Beeumen, J.J. / Feller, G.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Study of the active site residues of a glycoside hydrolase family 8 xylanase
Authors: Collins, T. / De Vos, D. / Hoyoux, A. / Savvides, S.N. / Gerday, C. / Van Beeumen, J. / Feller, G.
History
DepositionNov 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)46,0241
Polymers46,0241
Non-polymers00
Water11,097616
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.605, 91.620, 98.016
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 endo-1,4-beta-xylanase


Mass: 46023.785 Da / Num. of mol.: 1 / Mutation: D281N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria)
Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8RJN8, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2004
RadiationMonochromator: Triangular mono chromator(Bent mirror) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 114864 / Num. obs: 104895 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.3→1.34 Å / % possible all: 84.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.525 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14302 5309 5.1 %RANDOM
Rwork0.1225 ---
all0.12354 99620 --
obs0.12354 99620 91.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 0 616 3929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213410
X-RAY DIFFRACTIONr_bond_other_d0.0030.022835
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9054636
X-RAY DIFFRACTIONr_angle_other_deg1.00436646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035403
X-RAY DIFFRACTIONr_chiral_restr0.0950.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.023862
X-RAY DIFFRACTIONr_gen_planes_other0.0230.02734
X-RAY DIFFRACTIONr_nbd_refined0.2430.2660
X-RAY DIFFRACTIONr_nbd_other0.2460.23131
X-RAY DIFFRACTIONr_nbtor_other0.0820.21608
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2374
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3750.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.225
X-RAY DIFFRACTIONr_mcbond_it1.0431.52025
X-RAY DIFFRACTIONr_mcangle_it1.60223262
X-RAY DIFFRACTIONr_scbond_it2.12631385
X-RAY DIFFRACTIONr_scangle_it3.0674.51374
X-RAY DIFFRACTIONr_rigid_bond_restr1.0923410
X-RAY DIFFRACTIONr_sphericity_free3.4342616
X-RAY DIFFRACTIONr_sphericity_bonded2.29923313
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.219 349
Rwork0.18 6744

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