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- PDB-7ze9: Structure of an AA16 LPMO-like protein -

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Basic information

Entry
Database: PDB / ID: 7ze9
TitleStructure of an AA16 LPMO-like protein
ComponentsChitin-binding type-4 domain-containing protein
KeywordsMETAL BINDING PROTEIN / Carbohydrate Active Enzyme / Auxillary Activity / LPMO / AA16
Function / homology: / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / metal ion binding / ACETATE ION / COPPER (II) ION / Chitin-binding type-4 domain-containing protein
Function and homology information
Biological speciesThermothelomyces thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.646 Å
AuthorsHuang, Z. / Banerjee, S. / Muderspach, S.J. / Sun, P. / van Berkel, W.J.H. / Kabel, M.A. / Lo Leggio, L.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Denmark
Danish Council for Independent Research8021-00273B Denmark
CitationJournal: Acs Catalysis / Year: 2023
Title: AA16 Oxidoreductases Boost Cellulose-Active AA9 Lytic Polysaccharide Monooxygenases from Myceliophthora thermophila.
Authors: Sun, P. / Huang, Z. / Banerjee, S. / Kadowaki, M.A.S. / Veersma, R.J. / Magri, S. / Hilgers, R. / Muderspach, S.J. / Laurent, C.V.F.P. / Ludwig, R. / Cannella, D. / Lo Leggio, L. / van ...Authors: Sun, P. / Huang, Z. / Banerjee, S. / Kadowaki, M.A.S. / Veersma, R.J. / Magri, S. / Hilgers, R. / Muderspach, S.J. / Laurent, C.V.F.P. / Ludwig, R. / Cannella, D. / Lo Leggio, L. / van Berkel, W.J.H. / Kabel, M.A.
History
DepositionMar 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 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

Downloads & links

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Assembly

Deposited unit
AAA: Chitin-binding type-4 domain-containing protein
BBB: Chitin-binding type-4 domain-containing protein
CCC: Chitin-binding type-4 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,82713
Polymers61,5333
Non-polymers4,29410
Water2,720151
1
AAA: Chitin-binding type-4 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0314
Polymers20,5111
Non-polymers1,5203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Chitin-binding type-4 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0314
Polymers20,5111
Non-polymers1,5203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Chitin-binding type-4 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7665
Polymers20,5111
Non-polymers1,2554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.424, 52.154, 88.855
Angle α, β, γ (deg.)90.000, 105.666, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB CCC)

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Components

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Protein , 1 types, 3 molecules AAABBBCCC

#1: Protein Chitin-binding type-4 domain-containing protein


Mass: 20510.879 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothelomyces thermophilus (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2306267 / Production host: Thermothelomyces thermophilus (fungus) / References: UniProt: G2QH80

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Sugars , 3 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 3 types, 155 molecules

#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M buffer system 1 (1 M MES/ 1M Imidazole, pH 6.5), 45% EDO_P8K (40% w/v Ethylene glycol, 20% w/v PEG 8000), divalent cations (0.3 M Magnesium Chloride, O.3 M Calcium Chloride)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.646→85.554 Å / Num. obs: 19765 / % possible obs: 99.1 % / Redundancy: 4 % / CC1/2: 0.99 / Net I/σ(I): 10.5
Reflection shellResolution: 2.65→2.69 Å / Num. unique obs: 978 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold model

Resolution: 2.646→85.554 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.173 / SU B: 11.827 / SU ML: 0.235 / Average fsc free: 0.9014 / Average fsc work: 0.9184 / Cross valid method: FREE R-VALUE / ESU R: 0.742 / ESU R Free: 0.3
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2333 967 4.892 %
Rwork0.1776 18798 -
all0.18 --
obs-19765 99.053 %
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: 50.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0.471 Å2
2--2.542 Å20 Å2
3----2.064 Å2
Refinement stepCycle: LAST / Resolution: 2.646→85.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 288 152 4255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134234
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173573
X-RAY DIFFRACTIONr_angle_refined_deg1.661.7465792
X-RAY DIFFRACTIONr_angle_other_deg1.2441.6628366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3145487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76223.676204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8715555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.121515
X-RAY DIFFRACTIONr_chiral_restr0.0730.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024620
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02843
X-RAY DIFFRACTIONr_nbd_refined0.1990.2716
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.23184
X-RAY DIFFRACTIONr_nbtor_refined0.170.22023
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2123
X-RAY DIFFRACTIONr_metal_ion_refined0.1590.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.211
X-RAY DIFFRACTIONr_nbd_other0.1730.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.211
X-RAY DIFFRACTIONr_mcbond_it3.6045.2221967
X-RAY DIFFRACTIONr_mcbond_other3.5915.2191965
X-RAY DIFFRACTIONr_mcangle_it5.3457.8152445
X-RAY DIFFRACTIONr_mcangle_other5.3447.8172446
X-RAY DIFFRACTIONr_scbond_it4.8115.6742267
X-RAY DIFFRACTIONr_scbond_other4.815.6752268
X-RAY DIFFRACTIONr_scangle_it6.9618.3653347
X-RAY DIFFRACTIONr_scangle_other6.968.3663348
X-RAY DIFFRACTIONr_lrange_it8.81360.6274444
X-RAY DIFFRACTIONr_lrange_other8.81660.6374437
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
2.646-2.7150.334570.30913970.3114620.7560.79699.45280.294
2.715-2.7890.31580.26713680.26814300.8520.85899.72030.253
2.789-2.870.295740.23313040.23613840.8560.88599.56650.218
2.87-2.9580.292610.22312690.22613340.8780.89599.70010.205
2.958-3.0550.324650.22812320.23313020.8710.88999.6160.209
3.055-3.1620.32570.211800.20612390.8710.90799.83860.18
3.162-3.2810.284670.20511720.2112430.8930.91199.67820.189
3.281-3.4150.27710.18611010.19111780.9130.9499.49070.174
3.415-3.5670.244500.17810630.18111190.9190.95199.46380.171
3.567-3.740.193580.1610290.16210930.9550.95799.4510.155
3.74-3.9420.247460.1819630.18410200.930.94998.92160.173
3.942-4.1810.255440.1569260.1619830.9370.95498.67750.152
4.181-4.4690.194550.1338330.1369190.9510.96996.62680.135
4.469-4.8260.127300.1237830.1238500.9760.97395.64710.128
4.826-5.2850.22490.1317260.1368020.9480.97296.63340.136
5.285-5.9050.194330.156740.1527090.9570.97199.71790.159
5.905-6.8140.219260.1596260.1616560.9410.96699.39020.165
6.814-8.3320.27330.1585030.1645380.9170.95899.62830.17
8.332-11.7270.123220.1534080.1514350.9780.96698.85060.173
11.727-85.5540.192110.3062410.3012580.9150.90297.67440.352

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