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- PDB-7a8v: Crystal structure of Polysaccharide monooxygenase from P.verruculosum -

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Basic information

Entry
Database: PDB / ID: 7a8v
TitleCrystal structure of Polysaccharide monooxygenase from P.verruculosum
ComponentsLytic polysaccharide monooxygenase
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / P.verruculosum
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / hydrolase activity, acting on glycosyl bonds / cellulose catabolic process / monooxygenase activity / extracellular region
Similarity search - Function
Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
COPPER (II) ION / alpha-D-mannopyranose / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesTalaromyces verruculosus (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94961087137 Å
AuthorsNemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A.
Funding support1items
OrganizationGrant numberCountry
Russian Science Foundation
CitationJournal: To Be Published
Title: Crystal structure of Polysaccharide monooxygenase from P.verruculosum
Authors: Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A.
History
DepositionAug 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,28413
Polymers24,3681
Non-polymers1,91612
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-22 kcal/mol
Surface area10540 Å2
Unit cell
Length a, b, c (Å)132.145, 132.145, 39.952
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-309-

SO4

21A-309-

SO4

31A-650-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lytic polysaccharide monooxygenase


Mass: 24367.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces verruculosus (fungus) / Gene: lpmo1 / Production host: Penicillium canescens (fungus) / References: UniProt: A0A482A9N4

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Sugars , 2 types, 8 molecules

#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 261 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.13 Å3/Da / Density % sol: 70.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: cobalt chloride, MES, ammonium sulfate

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.94→33.04 Å / Num. obs: 29254 / % possible obs: 99 % / Redundancy: 4.04 % / Biso Wilson estimate: 10.7624280739 Å2 / Rmerge(I) obs: 0.1038 / Net I/σ(I): 10.28
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.2844 / Num. unique obs: 3860

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIS

4eis


Resolution: 1.94961087137→33.03625 Å / SU ML: 0.173506366293 / Cross valid method: FREE R-VALUE / σ(F): 1.34760157227 / Phase error: 16.3330556472
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186687473267 1467 5.01641362331 %
Rwork0.160537036731 27777 -
obs0.161874169645 29244 99.0583293815 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.3679876308 Å2
Refinement stepCycle: LAST / Resolution: 1.94961087137→33.03625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 114 257 2090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742129332491902
X-RAY DIFFRACTIONf_angle_d1.012666432052641
X-RAY DIFFRACTIONf_chiral_restr0.0582682084627323
X-RAY DIFFRACTIONf_plane_restr0.00615321169744328
X-RAY DIFFRACTIONf_dihedral_angle_d18.694951017685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94961087137-2.01930.2454486830791380.2112398386252607X-RAY DIFFRACTION93.5901807024
2.0193-2.10010.2091982741351470.1971647134662745X-RAY DIFFRACTION98.1004070556
2.1001-2.19570.2433289268151450.1844610581272735X-RAY DIFFRACTION99.3103448276
2.1957-2.31140.1987027667691440.1695178500452763X-RAY DIFFRACTION99.8625901752
2.3114-2.45620.2112629097991460.1743236428682795X-RAY DIFFRACTION99.9660095173
2.4562-2.64580.2094256972711470.1718666653152792X-RAY DIFFRACTION99.9659863946
2.6458-2.91190.195557748451500.1689976979422788X-RAY DIFFRACTION100
2.9119-3.33290.1818331297451510.1595621555452815X-RAY DIFFRACTION100
3.3329-4.19770.1497714531361470.13142112632820X-RAY DIFFRACTION100
4.1977-33.036250.1374856285851520.1225937955792917X-RAY DIFFRACTION99.7724317295

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