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- PDB-2dep: Crystal Structure of xylanase B from Clostridium stercorarium F9 -

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Basic information

Entry
Database: PDB / ID: 2dep
TitleCrystal Structure of xylanase B from Clostridium stercorarium F9
ComponentsThermostable celloxylanase
KeywordsHYDROLASE / GLYCOSIDASE / XYLAN DEGRADATION / FAMILY 10 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


cellulase / cellulase activity / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / 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
Thermostable celloxylanase
Similarity search - Component
Biological speciesClostridium stercorarium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFushinobu, S. / Nishimoto, M. / Miyanaga, A. / Kitaoka, M. / Hayashi, K.
Citation
Journal: To be Published
Title: Molecular anatomy of the alkaliphilic xylanase from Bacillus halodurans C-125
Authors: Nishimoto, M. / Fushinobu, S. / Miyanaga, A. / Kitaoka, M. / Hayashi, K.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Crystallization and preliminary X-ray analysis of xylanase B from Clostridium stercorarium
Authors: Nishimoto, M. / Fushinobu, S. / Miyanaga, A. / Wakagi, T. / Shoun, H. / Sakka, K. / Ohmiya, K. / Nirasawa, S. / Kitaoka, M. / Hayashi, K.
#2: Journal: Biosci.Biotechnol.Biochem. / Year: 2005
Title: The role of conserved arginine residue in loop 4 of glycoside hydrolase family 10 xylanases
Authors: Nishimoto, M. / Kitaoka, M. / Fushinobu, S. / Hayashi, K.
#3: Journal: J.Biosci.Bioeng. / Year: 2002
Title: Employing chimeric xylanases to identify regions of an alkaline xylanase participating in enzyme activity at basic pH
Authors: Nishimoto, M. / Kitaoka, M. / Hayashi, K.
History
DepositionFeb 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermostable celloxylanase
B: Thermostable celloxylanase


Theoretical massNumber of molelcules
Total (without water)82,7312
Polymers82,7312
Non-polymers00
Water12,755708
1
A: Thermostable celloxylanase


Theoretical massNumber of molelcules
Total (without water)41,3661
Polymers41,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thermostable celloxylanase


Theoretical massNumber of molelcules
Total (without water)41,3661
Polymers41,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.760, 96.600, 138.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thermostable celloxylanase / XYLANASE B


Mass: 41365.602 Da / Num. of mol.: 2 / Fragment: residues 41-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium stercorarium (bacteria) / Strain: F-9 / Gene: xynB / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P40942, cellulase, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24% PEG 1500, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 23, 2003 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50.14 Å / Num. all: 81152 / Num. obs: 80942 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.5 / Num. unique all: 8015 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HIZ

1hiz


Resolution: 1.8→50.14 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2018982.65 / 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
Rfree0.21 4085 5 %RANDOM
Rwork0.184 ---
all0.185 80942 --
obs0.184 80905 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.5148 Å2 / ksol: 0.388148 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å20 Å2
2--3.8 Å20 Å2
3----2.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→50.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 0 0 708 6256
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 680 5.1 %
Rwork0.243 12588 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.paramwater.top
X-RAY DIFFRACTION3water_rep.param

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