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- PDB-7pxv: LsAA9_A chemically reduced with ascorbic acid (high X-ray dose) -

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Basic information

Entry
Database: PDB / ID: 7pxv
TitleLsAA9_A chemically reduced with ascorbic acid (high X-ray dose)
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsTandrup, T. / Muderspach, S.J. / Banerjee, S. / 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)25,6646
Polymers25,2731
Non-polymers3915
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-38 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.410, 125.410, 125.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-661-

HOH

21A-666-

HOH

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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.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 3.5 M sodium chloride, 0.1 M citric acid pH 4.0 After the crystals were grown, they were transferred to a drop consisting of 3.5 M sodium chloride, 0.1 M citric acid pH 5.5, 0.01 M ascorbic ...Details: 3.5 M sodium chloride, 0.1 M citric acid pH 4.0 After the crystals were grown, they were transferred to a drop consisting of 3.5 M sodium chloride, 0.1 M citric acid pH 5.5, 0.01 M ascorbic acid pH 5.5 for 20 minutes before flash freezing

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→44.38 Å / Num. obs: 54321 / % possible obs: 100 % / Redundancy: 20.48 % / CC1/2: 0.999 / Rrim(I) all: 0.162 / Net I/σ(I): 16.65
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 21.19 % / Mean I/σ(I) obs: 2.27 / Num. unique obs: 3982 / CC1/2: 0.597 / Rrim(I) all: 2.752 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSFeb5, 2021 BUILT=20210323data reduction
XSCALEJan 31, 2020data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5ACH

5ach


Resolution: 1.5→44.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.33 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2753 5.1 %RANDOM
Rwork0.1874 ---
obs0.1884 51561 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.79 Å2 / Biso mean: 19.257 Å2 / Biso min: 9.88 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.5→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 18 269 2075
Biso mean--26.84 29.05 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131896
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171677
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.6472618
X-RAY DIFFRACTIONr_angle_other_deg1.4271.583867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62923.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.24815242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.525157
X-RAY DIFFRACTIONr_chiral_restr0.0820.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022230
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02435
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 202 -
Rwork0.283 3742 -
all-3944 -
obs--100 %

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