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- PDB-8b7p: Crystal structure of an AA9 LPMO from Aspergillus nidulans, AnLPMOC -

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Basic information

Entry
Database: PDB / ID: 8b7p
TitleCrystal structure of an AA9 LPMO from Aspergillus nidulans, AnLPMOC
ComponentsEndo-beta-1,4-glucanase D
KeywordsOXIDOREDUCTASE / Lytic polysaccharide monooxygenase / copper-binding protein / histidine brace
Function / homologyAuxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / COPPER (II) ION / Endo-beta-1,4-glucanase D
Function and homology information
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsMales, A. / Rafael Fanchini Terrasan, C. / Davies, G.J. / Walton, P.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004819/1 United Kingdom
CitationJournal: To Be Published
Title: Characterisation of lytic polysaccharide monooxygenases from Aspergillus nidulans
Authors: Rafael Fanchini Terrasan, C. / Males, A. / Figueiredo, F.L. / Gerhardt, J.A. / Rubio, M.V. / Franco Cairo, J.P. / Lindley, P. / Steward, M. / Lima Valadares, F. / Correa, T.L.R. / Davies, G. ...Authors: Rafael Fanchini Terrasan, C. / Males, A. / Figueiredo, F.L. / Gerhardt, J.A. / Rubio, M.V. / Franco Cairo, J.P. / Lindley, P. / Steward, M. / Lima Valadares, F. / Correa, T.L.R. / Davies, G.J. / Damasio, A. / Walton, P.H.
History
DepositionSep 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain ..._entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Endo-beta-1,4-glucanase D
BBB: Endo-beta-1,4-glucanase D
CCC: Endo-beta-1,4-glucanase D
DDD: Endo-beta-1,4-glucanase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,17214
Polymers89,9064
Non-polymers1,26610
Water4,720262
1
AAA: Endo-beta-1,4-glucanase D
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 22.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)22,7613
Polymers22,4771
Non-polymers2852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Endo-beta-1,4-glucanase D
hetero molecules


  • defined by author
  • 22.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)22,7613
Polymers22,4771
Non-polymers2852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Endo-beta-1,4-glucanase D
hetero molecules


  • defined by author
  • 22.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)22,8254
Polymers22,4771
Non-polymers3483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Endo-beta-1,4-glucanase D
hetero molecules


  • defined by author
  • 22.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)22,8254
Polymers22,4771
Non-polymers3483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.900, 64.378, 76.237
Angle α, β, γ (deg.)86.459, 85.540, 68.208
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Endo-beta-1,4-glucanase D / Endoglucanase D / Carboxymethylcellulase D / Cellulase D


Mass: 22476.584 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Gene: ANIA_06428 / Production host: Aspergillus nidulans (mold) / References: UniProt: Q5AZ52, cellulase
#2: 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.: 4 / 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
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium thiocyanate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.11→75.96 Å / Num. obs: 39040 / % possible obs: 80.5 % / Redundancy: 2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.097 / Net I/σ(I): 4.9
Reflection shellResolution: 2.11→2.17 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1271 / CC1/2: 0.779

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B5Q

4b5q


Resolution: 2.11→75.958 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.841 / SU B: 7.931 / SU ML: 0.206 / Cross valid method: FREE R-VALUE / ESU R: 0.391 / ESU R Free: 0.266
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.273 1947 4.988 %
Rwork0.2135 37090 -
all0.217 --
obs-39037 80.409 %
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: 16.227 Å2
Baniso -1Baniso -2Baniso -3
1--0.175 Å2-0.061 Å20.015 Å2
2--0.154 Å20.02 Å2
3----0.074 Å2
Refinement stepCycle: LAST / Resolution: 2.11→75.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 62 262 6620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136578
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175719
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.6649072
X-RAY DIFFRACTIONr_angle_other_deg1.2641.58813242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6495852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64124.12284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86715792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.641516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021430
X-RAY DIFFRACTIONr_nbd_refined0.1950.21265
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.25630
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23167
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2314
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0540.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.221
X-RAY DIFFRACTIONr_nbd_other0.2890.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.26
X-RAY DIFFRACTIONr_mcbond_it1.1411.7443408
X-RAY DIFFRACTIONr_mcbond_other1.1411.7443406
X-RAY DIFFRACTIONr_mcangle_it1.882.6114254
X-RAY DIFFRACTIONr_mcangle_other1.882.6114254
X-RAY DIFFRACTIONr_scbond_it1.1321.8033170
X-RAY DIFFRACTIONr_scbond_other1.1321.8033171
X-RAY DIFFRACTIONr_scangle_it1.8882.6894816
X-RAY DIFFRACTIONr_scangle_other1.8882.694817
X-RAY DIFFRACTIONr_lrange_it3.45520.6997177
X-RAY DIFFRACTIONr_lrange_other3.44920.6997159
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
2.11-2.1650.296480.23710510.23936210.8160.84130.35070.238
2.165-2.2240.297900.23716260.2435120.8290.85748.8610.237
2.224-2.2880.284630.24912440.25133860.8330.8438.60010.248
2.288-2.3590.3351270.2625610.26332760.7560.79582.05130.258
2.359-2.4360.3181470.25728320.26132120.7860.81492.7460.254
2.436-2.5210.2731450.21628850.21931120.8640.88697.3650.211
2.521-2.6160.2951320.23827580.24129610.8390.85497.60220.234
2.616-2.7230.42650.26913570.27628670.70.79949.59890.26
2.723-2.8440.2911350.22926030.23227830.8320.85598.3830.22
2.844-2.9830.2991390.23824340.24226210.8670.8798.16860.229
2.983-3.1440.2621340.23823080.23924880.8660.86598.15110.229
3.144-3.3340.3141220.23322440.23723960.8290.87698.74790.225
3.334-3.5640.2981120.22420780.22822230.90.91598.51550.221
3.564-3.8490.311010.20219490.20620850.850.90698.32130.198
3.849-4.2150.193660.16614550.16718870.9460.94680.60410.163
4.215-4.7110.212830.15216190.15517340.9490.96198.15460.153
4.711-5.4360.202740.15614380.15815310.9560.96498.7590.159
5.436-6.6490.217960.17311880.17712890.9540.95299.61210.176
6.649-9.3670.216340.1589530.169950.9440.96299.1960.162
9.367-75.9580.16340.1965070.1945450.9560.95699.26610.208

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