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- PDB-5msz: Lytic Polysaccharide Monooxygenase AA15 from Thermobia domestica ... -

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Basic information

Entry
Database: PDB / ID: 5msz
TitleLytic Polysaccharide Monooxygenase AA15 from Thermobia domestica in the Cu(I) State
ComponentsThermobia domestica domestica AA15
KeywordsOXIDOREDUCTASE / Lytic Polysaccharide Monooxygenase / CAZy / AA15 / Cellulose / Chitin / Copper
Function / homologyCellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / metal ion binding / COPPER (I) ION / Thermobia domestica domestica AA15
Function and homology information
Biological speciesThermobia domestica (firebrat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsHemsworth, G.R. / Sabbadin, F. / Ciano, L. / Henrissat, B. / Dupree, P. / Tryfona, T. / Besser, K. / Elias, L. / Pesante, G. / Li, Y. ...Hemsworth, G.R. / Sabbadin, F. / Ciano, L. / Henrissat, B. / Dupree, P. / Tryfona, T. / Besser, K. / Elias, L. / Pesante, G. / Li, Y. / Dowle, A. / Bates, R. / Gomez, L. / Hallam, R. / Davies, G.J. / Walton, P.H. / Bruce, N.C. / McQueen-Mason, S.
CitationJournal: Nat Commun / Year: 2018
Title: An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion.
Authors: Sabbadin, F. / Hemsworth, G.R. / Ciano, L. / Henrissat, B. / Dupree, P. / Tryfona, T. / Marques, R.D.S. / Sweeney, S.T. / Besser, K. / Elias, L. / Pesante, G. / Li, Y. / Dowle, A.A. / Bates, ...Authors: Sabbadin, F. / Hemsworth, G.R. / Ciano, L. / Henrissat, B. / Dupree, P. / Tryfona, T. / Marques, R.D.S. / Sweeney, S.T. / Besser, K. / Elias, L. / Pesante, G. / Li, Y. / Dowle, A.A. / Bates, R. / Gomez, L.D. / Simister, R. / Davies, G.J. / Walton, P.H. / Bruce, N.C. / McQueen-Mason, S.J.
History
DepositionJan 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry
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: Thermobia domestica domestica AA15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6144
Polymers22,4271
Non-polymers1883
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-5 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.985, 56.868, 66.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

#1: Protein Thermobia domestica domestica AA15


Mass: 22426.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobia domestica (firebrat) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R2JFH0*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 0.1 M LiCl, and 10 to 25% w/v polyethylene glycol 6000 (PEG-6000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection

Entry-ID: 5MSZ

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)
2-66.871266510054.10.9980.122144.3
1.1-56.877286699.63.80.9960.07328
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2-2.05570.15131.80.9981100
1.1-1.123.80.7521.60.637299.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→56.87 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.949 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15417 3694 5.1 %RANDOM
Rwork0.1329 ---
obs0.13399 69121 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2--0.36 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.1→56.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 9 209 1714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191612
X-RAY DIFFRACTIONr_bond_other_d0.0020.021427
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.932203
X-RAY DIFFRACTIONr_angle_other_deg0.99733288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09524.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8115241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3771512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211920
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02408
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_mcbond_it1.7381.422799
X-RAY DIFFRACTIONr_mcbond_other1.7291.417798
X-RAY DIFFRACTIONr_mcangle_it2.3322.1431002
X-RAY DIFFRACTIONr_mcangle_other2.3392.1471003
X-RAY DIFFRACTIONr_scbond_it1.911.53812
X-RAY DIFFRACTIONr_scbond_other1.9091.53812
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3722.2361192
X-RAY DIFFRACTIONr_long_range_B_refined4.01618.1371869
X-RAY DIFFRACTIONr_long_range_B_other4.01518.1471870
X-RAY DIFFRACTIONr_rigid_bond_restr1.9333036
X-RAY DIFFRACTIONr_sphericity_free23.8265124
X-RAY DIFFRACTIONr_sphericity_bonded9.00853071
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 269 -
Rwork0.234 5069 -
obs--99.79 %

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