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- PDB-1vbu: Crystal structure of native xylanase 10B from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1vbu
TitleCrystal structure of native xylanase 10B from Thermotoga maritima
Componentsendo-1,4-beta-xylanase B
KeywordsHYDROLASE / xylanase 10B
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide 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
ACETIC ACID / Beta-xylanase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIhsanawati / Kumasaka, T. / Kaneko, T. / Nakamura, S. / Tanaka, N.
Citation
Journal: Proteins / Year: 2005
Title: Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8
Authors: Ihsanawati / Kumasaka, T. / Kaneko, T. / Morokuma, C. / Yatsunami, R. / Sato, T. / Nakamura, S. / Tanaka, N.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Crystallization and preliminary X-ray studies of xylanse 10B from Thermotoga maritima
Authors: Ihsanawati / Kumasaka, T. / Kaneko, T. / Morokuma, C. / Nakamura, S. / Tanaka, N.
History
DepositionMar 2, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: endo-1,4-beta-xylanase B
B: endo-1,4-beta-xylanase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,04211
Polymers77,4022
Non-polymers6419
Water11,133618
1
A: endo-1,4-beta-xylanase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1297
Polymers38,7011
Non-polymers4286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: endo-1,4-beta-xylanase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9134
Polymers38,7011
Non-polymers2123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.500, 59.100, 61.340
Angle α, β, γ (deg.)84.59, 71.14, 68.32
Int Tables number1
Space group name H-MP1

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Components

#1: Protein endo-1,4-beta-xylanase B / Xylanase / xylanase 10B


Mass: 38700.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXS5, endo-1,4-beta-xylanase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.2 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: PEG 8000, sodium acetate, lithium sulfate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→57 Å / Num. all: 64816 / Num. obs: 64816 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.1 Å2
Reflection shellResolution: 1.8→1.87 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.53 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1006234.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3267 5 %RANDOM
Rwork0.186 ---
obs0.191 64809 96.7 %-
all-64809 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1769 Å2 / ksol: 0.376806 e/Å3
Displacement parametersBiso mean: 14.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20.03 Å2-1.21 Å2
2--0.67 Å2-0.37 Å2
3---1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5406 0 41 618 6065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 542 5.1 %
Rwork0.234 10134 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ACY_XPLOR.PARAMACY_XPLOR.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5GOL.PARAMGOL.TOP

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