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- PDB-7pxt: Structure of an LPMO, collected from serial synchrotron crystallo... -

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Basic information

Entry
Database: PDB / ID: 7pxt
TitleStructure of an LPMO, collected from serial synchrotron crystallography data.
ComponentsAuxiliary activity 9
KeywordsOXIDOREDUCTASE / Copper binding protein / Beta-sandwich fold / Auxillary
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / 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: 2.4 Å
AuthorsTandrup, T. / Santoni, G. / 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)25,5583
Polymers25,2731
Non-polymers2852
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-10 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.420, 125.420, 125.420
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-632-

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, lytic cellulose monooxygenase (C4-dehydrogenating)
#2: 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
#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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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, sitting drop / pH: 4
Details: 4.1 M NaCl, 0.1 M citric acid pH 4.0 The crystals were equilibrated in a drop of 3.5 M NaCl, 0.1 M citric acid pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→39.69 Å / Num. obs: 21952 / % possible obs: 88 % / Redundancy: 3.51 % / CC1/2: 0.619 / Rrim(I) all: 0.293 / Net I/σ(I): 7.21
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.59 % / Mean I/σ(I) obs: 3.37 / Num. unique obs: 1698 / CC1/2: 0.664 / Rrim(I) all: 0.91 / % possible all: 89.7
Serial crystallography sample deliveryDescription: mesh and collect routine / Method: fixed target
Serial crystallography sample delivery fixed targetSample holding: MicroMesh loop

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Processing

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

5ach


Resolution: 2.4→39.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.629 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 713 5.4 %RANDOM
Rwork0.1867 ---
obs0.19 12537 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.97 Å2 / Biso mean: 21.366 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.4→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 15 245 2048
Biso mean--35.74 20.99 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131866
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171654
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.6512577
X-RAY DIFFRACTIONr_angle_other_deg1.231.583812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1735236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5123.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47315241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.539157
X-RAY DIFFRACTIONr_chiral_restr0.0580.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022189
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
LS refinement shellResolution: 2.4→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 44 -
Rwork0.289 937 -
all-981 -
obs--97.03 %

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