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- PDB-6y0h: High resolution structure of GH11 xylanase from Nectria haematococca -

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Basic information

Entry
Database: PDB / ID: 6y0h
TitleHigh resolution structure of GH11 xylanase from Nectria haematococca
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / Xylanase / Atomic resolution / Nectria haematococca
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 species[Nectria] haematococca mpVI 77-13-4 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 Å
AuthorsAndaleeb, H. / Betzel, C. / Perbandt, M. / Brognaro, H.
CitationJournal: Sci Rep / Year: 2020
Title: High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca.
Authors: Andaleeb, H. / Ullah, N. / Falke, S. / Perbandt, M. / Brognaro, H. / Betzel, C.
History
DepositionFeb 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,9171
Polymers20,9171
Non-polymers00
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.446, 38.500, 53.591
Angle α, β, γ (deg.)90.000, 91.430, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

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Components

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


Mass: 20917.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: endo-1,4-beta-xylanase activity
Source: (gene. exp.) [Nectria] haematococca mpVI 77-13-4 (fungus)
Gene: NECHADRAFT_106153 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7YSL3, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1 M Ammonium sulphate,100mM Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1→34.67 Å / Num. obs: 82307 / % possible obs: 93.3 % / Redundancy: 3.2 % / CC1/2: 0.99 / Net I/σ(I): 15.5
Reflection shellResolution: 1→1.06 Å / Num. unique obs: 11904 / CC1/2: 0.85

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JRM

5jrm


Resolution: 1→34.67 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.897 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.025
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1535 4214 5.1 %RANDOM
Rwork0.1417 ---
obs0.1423 77789 92.92 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 63.58 Å2 / Biso mean: 9.386 Å2 / Biso min: 4.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.29 Å2
2---0.43 Å20 Å2
3---0.39 Å2
Refinement stepCycle: final / Resolution: 1→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 0 283 1742
Biso mean---23.23 -
Num. residues----189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191647
X-RAY DIFFRACTIONr_bond_other_d0.0010.021355
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.832287
X-RAY DIFFRACTIONr_angle_other_deg1.1152.9293178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1135235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96723.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.38615233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.267159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021993
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02388
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.45833002
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1→1.023 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.231 398 -
Rwork0.25 4450 -
obs--74.64 %

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