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- PDB-7pu1: High resolution X-ray structure of Thermoascus aurantiacus LPMO -

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Basic information

Entry
Database: PDB / ID: 7pu1
TitleHigh resolution X-ray structure of Thermoascus aurantiacus LPMO
ComponentsGh61 isozyme a
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 speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsBanerjee, S. / Frandsen, K.E.H. / Singh, R.K. / Bjerrum, M.J. / 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 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Gh61 isozyme a
BBB: Gh61 isozyme a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,07925
Polymers48,8362
Non-polymers1,24323
Water12,701705
1
AAA: Gh61 isozyme a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,02212
Polymers24,4181
Non-polymers60411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Gh61 isozyme a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,05713
Polymers24,4181
Non-polymers63912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.653, 89.046, 70.470
Angle α, β, γ (deg.)90.000, 103.335, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#1: Protein Gh61 isozyme a


Mass: 24418.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: G3XAP7, cellulase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#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.: 2 / 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


Mass: 35.453 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 20m M MgCl2 and 22 %(w/v) polyacrylic acid 5100 sodium salt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9538 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 1.06→37.34 Å / Num. obs: 171807 / % possible obs: 84.2 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rrim(I) all: 0.054 / Net I/σ(I): 18.57
Reflection shellResolution: 1.06→1.1 Å / Mean I/σ(I) obs: 3.6 / Num. unique obs: 12524 / CC1/2: 0.89 / Rrim(I) all: 0.44

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
TRUNCATEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YET

2yet


Resolution: 1.06→37.37 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / WRfactor Rfree: 0.144 / WRfactor Rwork: 0.118 / SU B: 0.651 / SU ML: 0.014 / Average fsc free: 0.9715 / Average fsc work: 0.9751 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.11851 8758 5.097 %
Rwork0.11735 163069 -
all0.119 --
obs-163069 84.244 %
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: 12.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.072 Å20 Å20.194 Å2
2---0.221 Å2-0 Å2
3---0.052 Å2
Refinement stepCycle: LAST / Resolution: 1.06→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 49 719 4213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0133731
X-RAY DIFFRACTIONr_bond_other_d0.0070.0173256
X-RAY DIFFRACTIONr_angle_refined_deg2.3041.6575188
X-RAY DIFFRACTIONr_angle_other_deg1.6241.5717658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.1325.423520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.73125.605157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88615494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.868153
X-RAY DIFFRACTIONr_chiral_restr0.1290.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025153
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02699
X-RAY DIFFRACTIONr_nbd_refined0.2530.2709
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.23236
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21848
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.10.21675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2451
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.27
X-RAY DIFFRACTIONr_nbd_other0.1030.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.259
X-RAY DIFFRACTIONr_mcbond_it1.3761.1361873
X-RAY DIFFRACTIONr_mcbond_other1.3561.1331871
X-RAY DIFFRACTIONr_mcangle_it1.8341.7172351
X-RAY DIFFRACTIONr_mcangle_other1.821.7162351
X-RAY DIFFRACTIONr_scbond_it3.6251.3291858
X-RAY DIFFRACTIONr_scbond_other3.6241.3291859
X-RAY DIFFRACTIONr_scangle_it3.241.9182814
X-RAY DIFFRACTIONr_scangle_other3.241.9192815
X-RAY DIFFRACTIONr_lrange_it3.71516.284399
X-RAY DIFFRACTIONr_lrange_other3.27114.9494165
X-RAY DIFFRACTIONr_rigid_bond_restr8.90636987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.0880.3022270.274658X-RAY DIFFRACTION32.4563
1.088-1.1170.1893620.1686568X-RAY DIFFRACTION47.2973
1.117-1.150.1694010.1458183X-RAY DIFFRACTION60.0784
1.15-1.1850.1514840.1279895X-RAY DIFFRACTION75.0959
1.185-1.2240.1526540.12211888X-RAY DIFFRACTION93.1936
1.224-1.2670.1236230.10411680X-RAY DIFFRACTION94.6603
1.267-1.3150.1336250.10711293X-RAY DIFFRACTION95.0929
1.315-1.3680.1236350.08710928X-RAY DIFFRACTION95.6489
1.368-1.4290.1215980.08210513X-RAY DIFFRACTION95.9416
1.429-1.4990.1115630.08110168X-RAY DIFFRACTION96.606
1.499-1.580.1135080.0789699X-RAY DIFFRACTION96.9878
1.58-1.6760.1134980.089195X-RAY DIFFRACTION97.2509
1.676-1.7910.1254340.098754X-RAY DIFFRACTION97.7759
1.791-1.9350.1214070.1068101X-RAY DIFFRACTION97.7594
1.935-2.1190.1344160.1147514X-RAY DIFFRACTION98.4971
2.119-2.3690.1313510.1186827X-RAY DIFFRACTION98.5718
2.369-2.7350.1443450.1276015X-RAY DIFFRACTION99.0809
2.735-3.3480.1562930.1365108X-RAY DIFFRACTION99.2284
3.348-4.730.1552160.1363956X-RAY DIFFRACTION98.6055
4.73-37.370.1991180.192126X-RAY DIFFRACTION95.0445

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