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- PDB-2g3i: Structure of S.olivaceoviridis xylanase Q88A/R275A mutant -

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Basic information

Entry
Database: PDB / ID: 2g3i
TitleStructure of S.olivaceoviridis xylanase Q88A/R275A mutant
ComponentsXylanase
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process
Similarity search - Function
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 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. ...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 / 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
PHOSPHATE ION / Beta-xylanase
Similarity search - Component
Biological speciesStreptomyces olivaceoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsDiertavitian, S. / Kaneko, S. / Fujimoto, Z. / Kuno, A. / Johansson, E. / Lo Leggio, L.
CitationJournal: PROCESS BIOCHEM / Year: 2012
Title: Structure-based engineering of glucose specificity in a family 10 xylanase from Streptomyces olivaceoviridis E-86
Authors: Ichinose, H. / Diertavitian, S. / Fujimoto, Z. / Kuno, A. / Leggio, L.L. / Kaneko, S.
History
DepositionFeb 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6998
Polymers34,0341
Non-polymers6657
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.317, 119.317, 54.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-1024-

HOH

21A-1108-

HOH

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Components

#1: Protein Xylanase /


Mass: 34034.383 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: Q88A/R275A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria)
Strain: E-86 / Gene: Xylanase / Plasmid: PET28A (Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q7SI98, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.4 Å3/Da / Density % sol: 63.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.1M ammonium dehydrogen phosphate, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.999 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 25881 / % possible obs: 99.5 % / Redundancy: 8.4 % / Rsym value: 0.179 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.511 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0001refinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: same protein in different crystal form

Resolution: 2.1→19.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.249 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2611 10.1 %RANDOM
Rwork0.155 ---
obs0.156 25843 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 35 233 2577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212415
X-RAY DIFFRACTIONr_bond_other_d0.0010.022046
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.913285
X-RAY DIFFRACTIONr_angle_other_deg0.87534749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7055302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13524.118119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32815367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.081517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
X-RAY DIFFRACTIONr_nbd_refined0.2130.2487
X-RAY DIFFRACTIONr_nbd_other0.1830.22069
X-RAY DIFFRACTIONr_nbtor_other0.0840.21324
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2189
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.214
X-RAY DIFFRACTIONr_mcbond_it0.9111.51918
X-RAY DIFFRACTIONr_mcbond_other0.1851.5633
X-RAY DIFFRACTIONr_mcangle_it1.0922388
X-RAY DIFFRACTIONr_scbond_it1.7931094
X-RAY DIFFRACTIONr_scangle_it2.6434.5897
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.232 219
Rwork0.183 1668
obs-1887

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