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- PDB-8yyo: Crystal structure of TsaGH11 complexed with beta-D-xylopyranose (... -

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Basic information

Entry
Database: PDB / ID: 8yyo
TitleCrystal structure of TsaGH11 complexed with beta-D-xylopyranose (Data II)
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / GH11 / xylanase / xylose / complex
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETATE ION / beta-D-xylopyranose / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoanaerobacterium saccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: Crystals / Year: 2024
Title: Recognition of a Single Beta-D-Xylopyranose Molecule by Xylanase GH11 from Thermoanaerobacterium saccharolyticum.
Authors: Nam, K.H.
History
DepositionApr 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,6895
Polymers40,3302
Non-polymers3593
Water7,314406
1
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3743
Polymers20,1651
Non-polymers2092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint0 kcal/mol
Surface area7480 Å2
MethodPISA
2
B: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3152
Polymers20,1651
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.226, 73.226, 164.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-205-

TYR

21A-205-

TYR

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Components

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


Mass: 20164.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria)
Gene: Tsac_0897 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3VTR8
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 49993 / % possible obs: 99.7 % / Redundancy: 18.7 % / CC1/2: 0.996 / Net I/σ(I): 9.98
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 2406 / CC1/2: 0.623

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→49.4 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 2000 4 %
Rwork0.1652 --
obs0.1663 49944 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 24 406 3272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062969
X-RAY DIFFRACTIONf_angle_d0.8534074
X-RAY DIFFRACTIONf_dihedral_angle_d7.294411
X-RAY DIFFRACTIONf_chiral_restr0.059427
X-RAY DIFFRACTIONf_plane_restr0.006518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.26721330.24563190X-RAY DIFFRACTION95
1.74-1.790.24781400.21973360X-RAY DIFFRACTION100
1.79-1.840.23811410.20343374X-RAY DIFFRACTION100
1.84-1.90.22861410.19063365X-RAY DIFFRACTION100
1.9-1.970.2491410.1823402X-RAY DIFFRACTION100
1.97-2.050.21681420.1613399X-RAY DIFFRACTION100
2.05-2.140.17331410.16183381X-RAY DIFFRACTION100
2.14-2.250.21411430.16273434X-RAY DIFFRACTION100
2.25-2.40.22511420.17293409X-RAY DIFFRACTION100
2.4-2.580.19571430.17243432X-RAY DIFFRACTION100
2.58-2.840.21671450.17133459X-RAY DIFFRACTION100
2.84-3.250.19231450.16543479X-RAY DIFFRACTION100
3.25-4.10.15191480.14143546X-RAY DIFFRACTION100
4.1-49.40.16081550.14633714X-RAY DIFFRACTION100

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