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- PDB-7ptz: High resolution X-ray structure of E. coli expressed Lentinus sim... -

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Basic information

Entry
Database: PDB / ID: 7ptz
TitleHigh resolution X-ray structure of E. coli expressed Lentinus similis LPMO.
ComponentsAuxiliary activity 9
KeywordsCARBOHYDRATE / LPMO / Monooxygenase / high resolution / Auxillary activity
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 / MOLECULAR REPLACEMENT / Resolution: 1.093 Å
AuthorsBanerjee, S. / Muderspach, S.J. / Tandrup, T. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, H.H.M. / Johansen, K.S. / Lo Leggio, L.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Sweden
Danish Council for Independent Research8021-00273B Sweden
Swedish Research Council2018-04969; 2019-02496 Sweden
CitationJournal: Biomolecules / Year: 2022
Title: Protonation State of an Important Histidine from High Resolution Structures of Lytic Polysaccharide Monooxygenases.
Authors: Banerjee, S. / Muderspach, S.J. / Tandrup, T. / Frandsen, K.E.H. / Singh, R.K. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, M.H.H. / Bjerrum, M.J. / Johansen, K.S. / Lo Leggio, L.
History
DepositionSep 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
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

Downloads & links

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Assembly

Deposited unit
AAA: Auxiliary activity 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5017
Polymers25,2601
Non-polymers2416
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.659, 48.659, 109.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Auxiliary activity 9


Mass: 25259.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinus similis (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S2GKZ1
#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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.59 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1 M citric acid pH 3.5 and 3.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.09→48.5 Å / Num. obs: 96541 / % possible obs: 91.3 % / Redundancy: 11.99 % / CC1/2: 0.99 / Rrim(I) all: 0.059 / Net I/σ(I): 19.3
Reflection shellResolution: 1.09→1.16 Å / Num. unique obs: 10733 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PQR

7pqr


Resolution: 1.093→48.5 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.984 / WRfactor Rfree: 0.144 / WRfactor Rwork: 0.124 / SU B: 0.814 / SU ML: 0.017 / Average fsc free: 0.9402 / Average fsc work: 0.9418 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.025
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1393 4828 5.025 %
Rwork0.1235 91248 -
all0.124 --
obs-96076 91.614 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.228 Å2
Baniso -1Baniso -2Baniso -3
1-0.445 Å2-0 Å2-0 Å2
2--0.445 Å2-0 Å2
3----0.891 Å2
Refinement stepCycle: LAST / Resolution: 1.093→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 7 360 2154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131930
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171650
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.6352678
X-RAY DIFFRACTIONr_angle_other_deg1.6621.5653850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20223.22996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.17315252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.481158
X-RAY DIFFRACTIONr_chiral_restr0.1390.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022266
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02402
X-RAY DIFFRACTIONr_nbd_refined0.2340.2394
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.21661
X-RAY DIFFRACTIONr_nbtor_refined0.180.2963
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.2893
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2199
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.212
X-RAY DIFFRACTIONr_nbd_other0.2880.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.228
X-RAY DIFFRACTIONr_mcbond_it2.4261.627977
X-RAY DIFFRACTIONr_mcbond_other2.2871.622976
X-RAY DIFFRACTIONr_mcangle_it2.8142.4491232
X-RAY DIFFRACTIONr_mcangle_other2.882.4541233
X-RAY DIFFRACTIONr_scbond_it3.1211.795953
X-RAY DIFFRACTIONr_scbond_other3.1031.784950
X-RAY DIFFRACTIONr_scangle_it2.8312.6351442
X-RAY DIFFRACTIONr_scangle_other2.7952.6311441
X-RAY DIFFRACTIONr_lrange_it3.44121.6212290
X-RAY DIFFRACTIONr_lrange_other3.30520.6812201
X-RAY DIFFRACTIONr_rigid_bond_restr6.04533580
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.093-1.1210.4281750.42334330.42477270.5050.49146.69340.41
1.121-1.1520.2732430.2949550.28975230.8210.79669.09480.281
1.152-1.1850.2463250.2256010.22273870.8830.89580.2220.209
1.185-1.2220.1923180.16660930.16871170.9260.93690.08010.151
1.222-1.2620.1463310.14264930.14269000.9530.9598.89850.122
1.262-1.3060.1543470.11963250.1266720.9540.9651000.101
1.306-1.3550.1343330.10661220.10764590.9730.97599.93810.09
1.355-1.4110.1343430.09758500.09961960.9740.9899.95160.083
1.411-1.4730.1172700.09257010.09359710.980.9831000.08
1.473-1.5450.1032800.08154020.08256830.9850.98899.98240.074
1.545-1.6290.1192740.08351590.08554340.9830.98899.98160.078
1.629-1.7270.1152620.08648660.08751280.9820.9871000.084
1.727-1.8460.1242030.09346130.09448160.9820.9861000.094
1.846-1.9940.1152540.09742150.09844690.9850.9871000.104
1.994-2.1840.1321990.10839410.10941410.9810.98499.97590.12
2.184-2.4410.1271910.11535760.11637670.9790.9811000.135
2.441-2.8180.1551660.13831230.13932900.9690.97399.96960.165
2.818-3.4480.1591290.13826740.13928050.9680.97599.92870.172
3.448-4.8640.1271250.12320340.12321740.9830.98299.310.157
4.864-48.50.163600.19110730.18912120.9690.96893.48180.247

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