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- PDB-1vbr: Crystal structure of complex xylanase 10B from Thermotoga maritim... -

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Basic information

Entry
Database: PDB / ID: 1vbr
TitleCrystal structure of complex xylanase 10B from Thermotoga maritima with xylobiose
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 studies of xylanase 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: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)78,32710
Polymers77,4022
Non-polymers9258
Water11,638646
1
A: endo-1,4-beta-xylanase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2236
Polymers38,7011
Non-polymers5225
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)39,1034
Polymers38,7011
Non-polymers4023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.460, 58.430, 61.290
Angle α, β, γ (deg.)70.43, 84.33, 68.77
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: Polysaccharide alpha-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 282.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a212h-1b_1-5][a212h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][a-D-Xylp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.15 Å3/Da / Density % sol: 42.27 %
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: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 4, 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→30 Å / Num. all: 64332 / Num. obs: 64332 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.9 Å2
Reflection shellResolution: 1.8→1.9 Å / % possible all: 96.2

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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→29.58 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1098872.58 / 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
Rfree0.215 6490 10.1 %RANDOM
Rwork0.181 ---
obs0.194 64329 97.2 %-
all-64329 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.0626 Å2 / ksol: 0.37956 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å22.31 Å2-5.87 Å2
2---5.33 Å2-1.73 Å2
3---4.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5406 0 38 670 6114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 1016 9.6 %
Rwork0.266 9609 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ACYL.PARAMACYL.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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