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- PDB-3wub: The wild type crystal structure of b-1,4-Xylanase (XynAS9) from S... -

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Basic information

Entry
Database: PDB / ID: 3wub
TitleThe wild type crystal structure of b-1,4-Xylanase (XynAS9) 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
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 1.1Jul 18, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9386
Polymers34,6111
Non-polymers3275
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.910, 80.910, 289.302
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 / Xylanase A


Mass: 34611.449 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-351
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 3.95 Å3/Da / Density % sol: 68.85 %
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) polyethylene glycol 8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→25 Å / Num. obs: 34597 / % possible obs: 99.3 % / Redundancy: 16.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 47.1
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 9.2 / Num. unique all: 3349 / % possible all: 99.1

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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: 3WUG

3wug


Resolution: 2.08→25 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 -RANDOM
Rwork0.196 --
all-32070 -
obs-30484 -
Refinement stepCycle: LAST / Resolution: 2.08→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 5 317 2764
LS refinement shellResolution: 2.08→2.15 Å
RfactorNum. reflection
Rfree0.227 2368
Rwork0.23 -
obs-32070

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