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- PDB-3ri8: Xylanase C from Aspergillus kawachii D37N mutant -

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Basic information

Entry
Database: PDB / ID: 3ri8
TitleXylanase C from Aspergillus kawachii D37N mutant
ComponentsEndo-1,4-beta-xylanase 3
KeywordsHYDROLASE / beta-jellyroll / Extracellular
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / 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 11/12, catalytic domain / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase 3
Similarity search - Component
Biological speciesAspergillus kawachii (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsFushinobu, S. / Uno, T. / Kitaoka, M. / Hayashi, K. / Matsuzawa, H. / Wakagi, T.
CitationJournal: J.APPL.GLYOSCI. / Year: 2011
Title: Mutational analysis of fungal family 11 xylanases on pH optimum determination
Authors: Fushinobu, S. / Uno, T. / Kitaoka, M. / Hayashi, K. / Matsuzawa, H. / Wakagi, T.
History
DepositionApr 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase 3


Theoretical massNumber of molelcules
Total (without water)20,0241
Polymers20,0241
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.064, 62.064, 113.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Endo-1,4-beta-xylanase 3 / Xylanase 3 / 1 / 4-beta-D-xylan xylanohydrolase 3 / Xylanase C


Mass: 20024.199 Da / Num. of mol.: 1 / Mutation: D37N
Source method: isolated from a genetically manipulated source
Details: Co-expression with pT-groE / Source: (gene. exp.) Aspergillus kawachii (mold) / Strain: IFO 4308 / Gene: xynC / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33557, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSWISSPROT CONTAINS ERRORS AT THESE POSITIONS

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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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M sodium sulfate, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 3, 1998
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→80 Å / Num. all: 15679 / Num. obs: 14918 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.041 / Net I/σ(I): 32.6
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 1304 / Rsym value: 0.359 / % possible all: 86.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
REFMAC5.5.0109refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1BK1

1bk1


Resolution: 2→34.7 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.183 / SU ML: 0.111 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 747 5 %RANDOM
Rwork0.16796 ---
all0.17084 14918 --
obs0.17084 14086 94.99 %-
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: 35.067 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.153 Å0.147 Å
Refinement stepCycle: LAST / Resolution: 2→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 0 77 1471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1221.8881965
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0585181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49724.50771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14315179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.83153
X-RAY DIFFRACTIONr_chiral_restr0.1460.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021152
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4011.5893
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49421431
X-RAY DIFFRACTIONr_scbond_it3.3483542
X-RAY DIFFRACTIONr_scangle_it4.9614.5534
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 49 -
Rwork0.331 908 -
obs--85.83 %

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