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- PDB-7ova: Crystal structure of an AA9 LPMO -

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Basic information

Entry
Database: PDB / ID: 7ova
TitleCrystal structure of an AA9 LPMO
ComponentsEndoglucanase, putative
KeywordsOXIDOREDUCTASE / LPMO / copper-dependent / monooxygenase
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 / (2S)-2-hydroxybutanedioic acid / AA9 family lytic polysaccharide monooxygenase
Similarity search - Component
Biological speciesNeosartorya fischeri (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMales, A. / Correa, T.L.R. / Murakami, M.T. / Walton, P.H. / Davies, G.J.
Funding support1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004819/1
CitationJournal: To Be Published
Title: Crystal structure of an AA9 LPMO
Authors: Correa, T.L.R. / Males, A. / Offen, W.A. / Murakami, M.T. / Walton, P.H. / Davies, G.J.
History
DepositionJun 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 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 6, 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: Endoglucanase, putative
BBB: Endoglucanase, putative
CCC: Endoglucanase, putative
DDD: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,45811
Polymers99,8024
Non-polymers6567
Water11,944663
1
AAA: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1483
Polymers24,9501
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0142
Polymers24,9501
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
CCC: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1483
Polymers24,9501
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
DDD: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1483
Polymers24,9501
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.510, 66.407, 86.700
Angle α, β, γ (deg.)83.711, 80.835, 89.995
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Endoglucanase, putative


Mass: 24950.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / CBS 544.65 / FGSC A1164 / JCM 1740 / NRRL 181 / WB 181) (mold)
Strain: ATCC 1020 / DSM 3700 / CBS 544.65 / FGSC A1164 / JCM 1740 / NRRL 181 / WB 181
Gene: NFIA_012990 / Production host: Escherichia coli (E. coli) / References: UniProt: A1D2G7
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 150 mM DL-Malic acid pH 7.0, 20% polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→49.55 Å / Num. obs: 80700 / % possible obs: 97.4 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.11 / Rrim(I) all: 0.148 / Net I/σ(I): 6.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4427 / CC1/2: 0.523 / Rpim(I) all: 0.555 / Rrim(I) all: 1.048 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZUD

3zud


Resolution: 1.75→49.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.147 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2264 3981 4.933 %
Rwork0.1836 76718 -
all0.186 --
obs-80699 97.445 %
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: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.339 Å20.064 Å20.086 Å2
2---0.82 Å20.45 Å2
3---1.195 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6819 0 31 663 7513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137066
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176200
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.6289651
X-RAY DIFFRACTIONr_angle_other_deg1.3811.57614369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4925922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81825.526304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.728151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.202154
X-RAY DIFFRACTIONr_chiral_restr0.070.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021558
X-RAY DIFFRACTIONr_nbd_refined0.2030.21290
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.25942
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23503
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2536
X-RAY DIFFRACTIONr_metal_ion_refined0.060.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.224
X-RAY DIFFRACTIONr_nbd_other0.1650.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.236
X-RAY DIFFRACTIONr_mcbond_it1.3691.7563664
X-RAY DIFFRACTIONr_mcbond_other1.3691.7553663
X-RAY DIFFRACTIONr_mcangle_it2.0692.6264576
X-RAY DIFFRACTIONr_mcangle_other2.0692.6284577
X-RAY DIFFRACTIONr_scbond_it1.7821.8773402
X-RAY DIFFRACTIONr_scbond_other1.7811.8763401
X-RAY DIFFRACTIONr_scangle_it2.7322.7515069
X-RAY DIFFRACTIONr_scangle_other2.7312.7515070
X-RAY DIFFRACTIONr_lrange_it4.02221.0598041
X-RAY DIFFRACTIONr_lrange_other4.02221.0628042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.2922960.2575619X-RAY DIFFRACTION96.0851
1.795-1.8450.2562830.2465458X-RAY DIFFRACTION96.0998
1.845-1.8980.2612740.2285296X-RAY DIFFRACTION96.1837
1.898-1.9560.2712460.2145225X-RAY DIFFRACTION96.6096
1.956-2.0210.2482520.1975012X-RAY DIFFRACTION96.8894
2.021-2.0910.2362450.1824913X-RAY DIFFRACTION97.1375
2.091-2.170.2262150.1824716X-RAY DIFFRACTION97.1052
2.17-2.2590.2422370.1794522X-RAY DIFFRACTION97.4406
2.259-2.3590.2222360.174367X-RAY DIFFRACTION97.418
2.359-2.4740.2292440.1734157X-RAY DIFFRACTION97.3242
2.474-2.6080.2451960.1793983X-RAY DIFFRACTION98.0986
2.608-2.7660.2072010.1723785X-RAY DIFFRACTION98.2257
2.766-2.9570.2141920.1793529X-RAY DIFFRACTION98.4913
2.957-3.1930.2271560.1813346X-RAY DIFFRACTION98.5369
3.193-3.4980.231630.1823050X-RAY DIFFRACTION98.892
3.498-3.910.2041590.1652750X-RAY DIFFRACTION99.0129
3.91-4.5130.1831250.1572452X-RAY DIFFRACTION98.5845
4.513-5.5230.1861190.1572069X-RAY DIFFRACTION99.229
5.523-7.7950.213770.1851603X-RAY DIFFRACTION99.7033
7.795-49.550.279650.203866X-RAY DIFFRACTION99.2537

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