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- PDB-2a8z: Structure Of A Cold-Adapted Family 8 Xylanase -

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Basic information

Entry
Database: PDB / ID: 2a8z
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: 3.2 Å
AuthorsCollins, T. / De Vos, D. / Hoyoux, A. / Savvides, S.N. / Gerday, C. / Van Beeumen, 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
DepositionJul 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: 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)45,9811
Polymers45,9811
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.779, 77.779, 149.634
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein endo-1,4-beta-xylanase


Mass: 45980.758 Da / Num. of mol.: 1 / Mutation: D144A
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.: 57 / 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: 2.8 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG8000, sodium cacodylate, ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8034 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2005
RadiationMonochromator: - Triangular mono chromator - Bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8034 Å / Relative weight: 1
ReflectionResolution: 3.2→12 Å / Num. all: 8932 / Num. obs: 8337 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.27 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1H13

1h13


Resolution: 3.2→12 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.832 / SU B: 22.902 / SU ML: 0.409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.588 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 392 4.7 %RANDOM
Rwork0.21607 ---
all0.21882 7938 --
obs0.21882 7938 93.56 %-
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: 26.668 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å22.32 Å20 Å2
2--4.64 Å20 Å2
3----6.96 Å2
Refinement stepCycle: LAST / Resolution: 3.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 0 57 3260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213299
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9084483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5695403
X-RAY DIFFRACTIONr_chiral_restr0.0770.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022635
X-RAY DIFFRACTIONr_nbd_refined0.2190.22032
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.27
X-RAY DIFFRACTIONr_mcbond_it0.4711.52002
X-RAY DIFFRACTIONr_mcangle_it0.88923178
X-RAY DIFFRACTIONr_scbond_it0.88731297
X-RAY DIFFRACTIONr_scangle_it1.5444.51305
LS refinement shellResolution: 3.201→3.278 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 37
Rwork0.249 545

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