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- PDB-3niy: Crystal structure of native xylanase 10B from Thermotoga petrophi... -

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Basic information

Entry
Database: PDB / ID: 3niy
TitleCrystal structure of native xylanase 10B from Thermotoga petrophila RKU-1
ComponentsEndo-1,4-beta-xylanaseXylanase
KeywordsHYDROLASE / TIM-barrel / xylanase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Beta-xylanase
Similarity search - Component
Biological speciesThermotoga petrophila RKU-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsSantos, C.R. / Meza, A.N. / Trindade, D.M. / Ruller, R. / Squina, F.M. / Prade, R.A. / Murakami, M.T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of ...Title: Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1.
Authors: Santos, C.R. / Meza, A.N. / Hoffmam, Z.B. / Silva, J.C. / Alvarez, T.M. / Ruller, R. / Giesel, G.M. / Verli, H. / Squina, F.M. / Prade, R.A. / Murakami, M.T.
History
DepositionJun 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,62312
Polymers80,8472
Non-polymers77610
Water11,097616
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9858
Polymers40,4241
Non-polymers5617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6384
Polymers40,4241
Non-polymers2143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.538, 58.554, 61.579
Angle α, β, γ (deg.)84.54, 70.82, 68.87
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Endo-1,4-beta-xylanase / Xylanase


Mass: 40423.723 Da / Num. of mol.: 2 / Fragment: UNP residues 21 to 344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga petrophila RKU-1 (bacteria) / Strain: RKU-1 / Gene: Tpet_0854 / Production host: Escherichia coli (E. coli) / References: UniProt: A5IL00, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: PEG8000 glycerol sodium acetate litium sulfate, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 3, 2010
RadiationMonochromator: silicon double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.58→31.24 Å / Num. all: 95840 / Num. obs: 91930 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.101
Reflection shellResolution: 1.58→1.64 Å / % possible all: 86.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→31.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.325 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19551 4584 5 %RANDOM
Rwork0.15792 ---
obs0.1598 87311 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.01 Å2-0.09 Å2
2--0.18 Å2-0.47 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.58→31.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 45 616 6101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0225638
X-RAY DIFFRACTIONr_angle_refined_deg2.4151.9417630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2795649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94324.463298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32815986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2971528
X-RAY DIFFRACTIONr_chiral_restr0.1870.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214348
X-RAY DIFFRACTIONr_mcbond_it1.5181.53261
X-RAY DIFFRACTIONr_mcangle_it2.46325275
X-RAY DIFFRACTIONr_scbond_it3.86532377
X-RAY DIFFRACTIONr_scangle_it6.164.52355
LS refinement shellResolution: 1.576→1.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 282 -
Rwork0.292 5793 -
obs--82.99 %

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