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- PDB-8af4: Room temperature SSX structure of GH11 xylanase from Nectria haem... -

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Basic information

Entry
Database: PDB / ID: 8af4
TitleRoom temperature SSX structure of GH11 xylanase from Nectria haematococca (40000 frames)
ComponentsEndo-1,4-beta-xylanaseXylanase
KeywordsHYDROLASE / Xylanase / SSX / TapeDrive / room temperature
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
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
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesFusarium haematococcum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsOberthuer, D. / Andaleeb, H. / Betzel, C. / Perbandt, M. / Yefanov, O. / Zielinski, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2022
Title: Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive.
Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, ...Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, T.A. / Fleckenstein, H. / Sarrou, I. / Werner, N. / Betzel, C. / Rohde, H. / Aepfelbacher, M. / Chapman, H.N. / Perbandt, M. / Steiner, R.A. / Oberthuer, D.
History
DepositionJul 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)20,5751
Polymers20,5751
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.550, 38.850, 53.570
Angle α, β, γ (deg.)90.000, 91.000, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-279-

HOH

21A-375-

HOH

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Components

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


Mass: 20575.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium haematococcum (fungus)
Strain: ATCC MYA-4622 / CBS 123669 / FGSC 9596 / NRRL 45880 / 77-13-4
Gene: NECHADRAFT_106153 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7YSL3, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.5
Details: For crystallization, the original conditions were modified to obtain microcrystals. Initial crystals obtained from hanging drops under the precipitant condition: 1 M ammonium sulfate, 100 mM ...Details: For crystallization, the original conditions were modified to obtain microcrystals. Initial crystals obtained from hanging drops under the precipitant condition: 1 M ammonium sulfate, 100 mM sodium citrate pH 5.5 were crushed under a stereomicroscope, using a crystal crusher tool (Hampton research). The reservoir solution was pipetted to the drop and the seed stock was collected by washing the drop with reservoir solution. The seed stock was transferred to a seed bead tube (Molecular Dimensions Ltd., UK), vortexed three times for 30 s each, with an interval of 30 s between each vortex, to get the final seed stock. Protein solution 15 mg/mL, precipitant solution, and seed stock were mixed with a ratio of 1:1:0.5. The mixture was vortexed for 30 s in ten-minute intervals. After 30 min, the microcrystals were centrifuged at 200 rpm and the supernatant was replaced with a precipitant solution. Applying the same protocol, microcrystals were obtained under two precipitant conditions i.e. Precipitant 1: 1M (NH4)2SO4, 100 mM sodium citrate pH 5.5, and Precipitant 2: 200 mM (NH4)2SO4, 100 mM sodium citrate pH 5.5 and 20% PEG 6000. Microcrystals obtained under both precipitant conditions were tested for diffraction data collection

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.51→17.16 Å / Num. obs: 25916 / % possible obs: 98.75 % / Redundancy: 432 % / Biso Wilson estimate: 19.51 Å2 / CC1/2: 0.987 / CC star: 0.997 / R split: 0.1342 / Net I/σ(I): 5.83
Reflection shellResolution: 1.51→1.54 Å / Mean I/σ(I) obs: 0.55 / Num. unique obs: 2291 / CC1/2: 0.152 / CC star: 0.514 / R split: 2.49 / % possible all: 87.48
Serial crystallography sample deliveryDescription: TapeDrive / Method: injection
Serial crystallography sample delivery injectionDescription: TapeDrive / Flow rate: 1 µL/min / Injector diameter: 180 µm / Injector temperature: 295 K
Serial crystallography data reductionFrames total: 40000 / Lattices indexed: 41508

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y0H

6y0h


Resolution: 1.51→17.16 Å / SU ML: 0.1996 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.4836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1831 1985 7.76 %
Rwork0.1516 23584 -
obs0.1541 25569 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.58 Å2
Refinement stepCycle: LAST / Resolution: 1.51→17.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 0 220 1679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941653
X-RAY DIFFRACTIONf_angle_d1.05912293
X-RAY DIFFRACTIONf_chiral_restr0.0618241
X-RAY DIFFRACTIONf_plane_restr0.0063305
X-RAY DIFFRACTIONf_dihedral_angle_d6.2582259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.3708980.3751098X-RAY DIFFRACTION63.68
1.55-1.590.36311380.32961684X-RAY DIFFRACTION99.56
1.59-1.640.30051420.29681715X-RAY DIFFRACTION99.79
1.64-1.690.31531470.27541739X-RAY DIFFRACTION99.84
1.69-1.750.28671480.23331712X-RAY DIFFRACTION99.95
1.75-1.820.28021450.22061715X-RAY DIFFRACTION100
1.82-1.90.22121440.18761700X-RAY DIFFRACTION100
1.9-20.22521390.15511741X-RAY DIFFRACTION100
2-2.130.18771480.14221731X-RAY DIFFRACTION100
2.13-2.290.1711450.12621741X-RAY DIFFRACTION100
2.29-2.520.18391430.13171724X-RAY DIFFRACTION100
2.52-2.880.16661470.13381741X-RAY DIFFRACTION100
2.88-3.630.13281480.11591745X-RAY DIFFRACTION100
3.63-17.160.13951530.12621798X-RAY DIFFRACTION99.85

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