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- PDB-3wug: The mutant crystal structure of b-1,4-Xylanase (XynAS9_V43P/G44E)... -

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Basic information

Entry
Database: PDB / ID: 3wug
TitleThe mutant crystal structure of b-1,4-Xylanase (XynAS9_V43P/G44E) with xylobiose from Streptomyces sp. 9
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / beta-1 / 4-xylanase / thermozyme / protein engineering / protein rigidity
Function / homology
Function and homology information


polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 ...Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4beta-beta-xylobiose / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsChen, C.C. / Han, X. / Lv, P. / Ko, T.P. / Peng, W. / Huang, C.H. / Zheng, Y. / Gao, J. / Yang, Y.Y. / Guo, R.T.
CitationJournal: J.Biotechnol. / Year: 2014
Title: Structural perspectives of an engineered beta-1,4-xylanase with enhanced thermostability.
Authors: Chen, C.C. / Luo, H. / Han, X. / Lv, P. / Ko, T.P. / Peng, W. / Huang, C.H. / Wang, K. / Gao, J. / Zheng, Y. / Yang, Y. / Zhang, J. / Yao, B. / Guo, R.T.
History
DepositionApr 23, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.ptnr1_label_seq_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,70410
Polymers34,6811
Non-polymers1,0229
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.798, 80.798, 288.589
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Endo-1,4-beta-xylanase A


Mass: 34681.492 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-351 / Mutation: V81P, G82E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: xynAS9 / Plasmid: pPIC9 / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: B4XVN1, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.5M zinc acetate dehydrate, 0.1M sodium cacodylate trihydrate pH 6.5, 8% (w/v) , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→25 Å / Num. obs: 46576 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 32
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CUI

3cui


Resolution: 1.88→25 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.215 -RANDOM
Rwork0.2 --
all-43327 -
obs-41158 -
Refinement stepCycle: LAST / Resolution: 1.88→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 45 316 2799
LS refinement shellResolution: 1.88→1.95 Å /
RfactorNum. reflection
Rfree0.29 3569
Rwork0.291 -

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