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- PDB-6z5y: Structure of a novel LPMO from Phytophthora infestans -

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Basic information

Entry
Database: PDB / ID: 6z5y
TitleStructure of a novel LPMO from Phytophthora infestans
ComponentsLytic Polysaccharide Monooxygenase
KeywordsMETAL BINDING PROTEIN / Lytic polysaccharide monooxygenase / copper / LPMO
Function / homologymetal ion binding / COPPER (II) ION / TRIETHYLENE GLYCOL / Mucin-like protein
Function and homology information
Biological speciesPhytophthora infestans (potato late blight agent)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.01 Å
AuthorsUrresti, S. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R007705/1 United Kingdom
CitationJournal: Science / Year: 2021
Title: Secreted pectin monooxygenases drive plant infection by pathogenic oomycetes.
Authors: Sabbadin, F. / Urresti, S. / Henrissat, B. / Avrova, A.O. / Welsh, L.R.J. / Lindley, P.J. / Csukai, M. / Squires, J.N. / Walton, P.H. / Davies, G.J. / Bruce, N.C. / Whisson, S.C. / McQueen-Mason, S.J.
History
DepositionMay 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lytic Polysaccharide Monooxygenase
B: Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3105
Polymers40,0332
Non-polymers2773
Water6,323351
1
A: Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2303
Polymers20,0171
Non-polymers2142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0802
Polymers20,0171
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.293, 45.458, 53.687
Angle α, β, γ (deg.)83.910, 71.850, 83.780
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lytic Polysaccharide Monooxygenase


Mass: 20016.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminus Strep tag sequence: WSHPQFEK
Source: (gene. exp.) Phytophthora infestans (strain T30-4) (eukaryote)
Gene: PITG_04949 / Production host: Escherichia coli (E. coli) / References: UniProt: D0N2F7
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.13 Å3/Da / Density % sol: 42.18 % / Description: Hollow rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20mM Tris pH 7.0, 22% Polyethylene Glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.01→28.79 Å / Num. obs: 156702 / % possible obs: 92.4 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.01-1.032.70.6867650.5890.5090.85680.9
5.53-28.773.80.0359920.9970.0210.04195.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
Fragonphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.01→28.79 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.791 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Residues 139-142 and 172-177 (chains A and B) show poor density and therefore low occupancy. C-terminal ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Residues 139-142 and 172-177 (chains A and B) show poor density and therefore low occupancy. C-terminal residues (172-177) correspond to a non cleaved Strep tag, and some have been built with no side chains.
RfactorNum. reflection% reflectionSelection details
Rfree0.164 7636 4.9 %RANDOM
Rwork0.143 ---
obs0.1441 148984 92.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 36.26 Å2 / Biso mean: 11.889 Å2 / Biso min: 5.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0.07 Å20.29 Å2
2--0.31 Å2-0.15 Å2
3----0.35 Å2
Refinement stepCycle: final / Resolution: 1.01→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 9 351 3043
Biso mean--16.51 18.75 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132980
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172594
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.6434104
X-RAY DIFFRACTIONr_angle_other_deg1.6021.5766097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4095410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50824.478134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43615454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.647158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023453
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02603
X-RAY DIFFRACTIONr_rigid_bond_restr2.71635574
LS refinement shellResolution: 1.01→1.036 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 556 -
Rwork0.269 9929 -
all-10485 -
obs--83.35 %

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