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- PDB-7pxr: Room temperature structure of an LPMO. -

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Basic information

Entry
Database: PDB / ID: 7pxr
TitleRoom temperature structure of an LPMO.
ComponentsAuxiliary activity 9
KeywordsOXIDOREDUCTASE / Copper binding protein / Beta-sandwich fold / Auxillary
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
: / Auxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesLentinus similis (fungus)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsTandrup, T. / Meilleur, F. / Ipsen, J. / Johansen, K.S. / Lo Leggio, L.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Denmark
Danish Council for Independent Research8021-00273B Denmark
CitationJournal: Iucrj / Year: 2022
Title: Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding.
Authors: Tandrup, T. / Muderspach, S.J. / Banerjee, S. / Santoni, G. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, M.H.H. / Johansen, K.S. / Meilleur, F. / Lo Leggio, L.
History
DepositionOct 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Auxiliary activity 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,01816
Polymers25,2731
Non-polymers74615
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-117 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.659, 126.659, 126.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Auxiliary activity 9 / LsAA9A / lytic polysaccharide monooxygenase


Mass: 25272.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinus similis (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A0S2GKZ1, EC: 1.14.99.56
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
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
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.35 Å3/Da / Density % sol: 63.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 3.0 M sodium chloride, 0.1 M citric acid pH 3.5 The crystals were soaked in a drop containing 3.0 M sodium chloride, 0.1 M citric acid pH 5.5 for 10 min before mounting

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Aug 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→29.87 Å / Num. obs: 32798 / % possible obs: 100 % / Redundancy: 17.2 % / CC1/2: 1 / Rrim(I) all: 0.047 / Net I/σ(I): 43.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1930 / CC1/2: 0.925 / Rrim(I) all: 0.509 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5ACH

5ach


Resolution: 1.8→29.87 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.698 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1662 1670 5.1 %RANDOM
Rwork0.1467 ---
obs0.1478 31034 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.03 Å2 / Biso mean: 20.874 Å2 / Biso min: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 28 182 1998
Biso mean--45.78 35.14 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131940
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171716
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.6462693
X-RAY DIFFRACTIONr_angle_other_deg1.4781.583970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26223.76393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78215253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.122157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022300
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02445
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 122 -
Rwork0.209 2239 -
all-2361 -
obs--99.96 %

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