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- PDB-7xs3: AlXyn26A E243A-X3X4X -

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Basic information

Entry
Database: PDB / ID: 7xs3
TitleAlXyn26A E243A-X3X4X
ComponentsAlXyn26A E243A-X3X4X
KeywordsHYDROLASE / MLXase / Mutant E243A / Complex / X3X4X
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesAlgibacter sp. L4_22 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, Y.Z. / Chen, X.L. / Zhao, F. / Yu, C.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: A novel class of xylanases specifically degrade marine red algal beta 1,3/1,4-mixed-linkage xylan.
Authors: Zhao, F. / Yu, C.M. / Sun, H.N. / Zhao, L.S. / Ding, H.T. / Cao, H.Y. / Chen, Y. / Qin, Q.L. / Zhang, Y.Z. / Li, P.Y. / Chen, X.L.
History
DepositionMay 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AlXyn26A E243A-X3X4X
B: AlXyn26A E243A-X3X4X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6674
Polymers77,8382
Non-polymers8292
Water11,385632
1
A: AlXyn26A E243A-X3X4X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3332
Polymers38,9191
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-2 kcal/mol
Surface area12610 Å2
MethodPISA
2
B: AlXyn26A E243A-X3X4X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3332
Polymers38,9191
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-2 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.419, 107.051, 118.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-653-

HOH

21B-734-

HOH

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Components

#1: Protein AlXyn26A E243A-X3X4X


Mass: 38919.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Algibacter sp. L4_22 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide beta-D-xylopyranose-(1-3)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DXylpb1-3DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(3+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.97 Å3/Da / Density % sol: 37.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→48.79 Å / Num. obs: 45545 / % possible obs: 92.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.055 / Net I/σ(I): 25.7
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.229 / Num. unique obs: 2349 / CC1/2: 0.923

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XJR

7xjr


Resolution: 1.9→31.8 Å / SU ML: 0.2122 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2197 1999 4.39 %
Rwork0.1709 43485 -
obs0.1731 45484 91.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 56 632 5684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00655220
X-RAY DIFFRACTIONf_angle_d0.79297078
X-RAY DIFFRACTIONf_chiral_restr0.0523706
X-RAY DIFFRACTIONf_plane_restr0.0059902
X-RAY DIFFRACTIONf_dihedral_angle_d8.7722690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30711150.23142493X-RAY DIFFRACTION74.49
1.95-20.26591310.20972843X-RAY DIFFRACTION86.28
2-2.060.26171430.19343129X-RAY DIFFRACTION93.25
2.06-2.130.27061220.18842680X-RAY DIFFRACTION80.82
2.13-2.20.26971540.18963331X-RAY DIFFRACTION99.32
2.2-2.290.25581330.19132907X-RAY DIFFRACTION86.98
2.29-2.390.26081530.18213315X-RAY DIFFRACTION99.46
2.39-2.520.23221530.19053331X-RAY DIFFRACTION99.4
2.52-2.680.24541540.18363348X-RAY DIFFRACTION99.18
2.68-2.880.26641530.18933335X-RAY DIFFRACTION99.18
2.88-3.170.23581540.1853354X-RAY DIFFRACTION98.82
3.17-3.630.19361380.16113000X-RAY DIFFRACTION88.22
3.63-4.570.16061360.13182950X-RAY DIFFRACTION85.25
4.58-31.80.17221600.14583469X-RAY DIFFRACTION96.11

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