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- PDB-7t5c: X-ray structure of Neurospora crassa Polysaccharide Monooxygenase... -

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Basic information

Entry
Database: PDB / ID: 7t5c
TitleX-ray structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) at low pH
ComponentsLytic polysaccharide monooxygenase
KeywordsOXIDOREDUCTASE / LPMO / monooxygenase / PMO / metalloproteins / copper
Function / homologyAuxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / monooxygenase activity / hydrolase activity / extracellular region / metal ion binding / COPPER (II) ION / Lytic polysaccharide monooxygenase
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSchroder, G.C. / Meilleur, F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)Hatch 211001 United States
National Research Foundation in South Africa United States
Department of Energy (DOE, United States) United States
Citation
Journal: Chem Sci / Year: 2022
Title: Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase.
Authors: Schroder, G.C. / O'Dell, W.B. / Webb, S.P. / Agarwal, P.K. / Meilleur, F.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2021
Title: Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions.
Authors: Schroder, G.C. / O'Dell, W.B. / Swartz, P.D. / Meilleur, F.
History
DepositionDec 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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

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Assembly

Deposited unit
A: Lytic polysaccharide monooxygenase
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7366
Polymers46,5982
Non-polymers1,1384
Water13,998777
1
A: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7873
Polymers23,2991
Non-polymers4882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9493
Polymers23,2991
Non-polymers6502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.668, 42.210, 69.715
Angle α, β, γ (deg.)90.000, 98.910, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Lytic polysaccharide monooxygenase / Related to cel1 protein


Mass: 23299.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G15G9.090, GE21DRAFT_7469 / Production host: Komagataella pastoris (fungus) / Strain (production host): SuperMan5 / References: UniProt: Q8WZQ2
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 1.96 Å3/Da / Density % sol: 41.73 % / Description: Crystals form rectangular shapes.
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.4 / Details: PEG 3350, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→12.61 Å / Num. obs: 62507 / % possible obs: 99.78 % / Redundancy: 8.2 % / Biso Wilson estimate: 11.79 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.1495 / Net I/σ(I): 62.56
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.2775 / Mean I/σ(I) obs: 7.14 / Num. unique obs: 6159 / CC1/2: 0.94 / Rrim(I) all: 0.3133 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TKH

5tkh


Resolution: 1.5→12.61 Å / SU ML: 0.1158 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 18.0267 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 3110 4.98 %Random selection
Rwork0.1556 59395 --
obs0.157 62505 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→12.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 69 777 4118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783673
X-RAY DIFFRACTIONf_angle_d1.0975082
X-RAY DIFFRACTIONf_chiral_restr0.0723588
X-RAY DIFFRACTIONf_plane_restr0.0087660
X-RAY DIFFRACTIONf_dihedral_angle_d15.55741362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.22381630.18342611X-RAY DIFFRACTION100
1.52-1.550.23381430.17532698X-RAY DIFFRACTION99.96
1.55-1.570.21531350.16822675X-RAY DIFFRACTION99.93
1.57-1.60.20711410.16992672X-RAY DIFFRACTION99.96
1.6-1.630.17441400.16172712X-RAY DIFFRACTION100
1.63-1.670.191410.16712662X-RAY DIFFRACTION100
1.67-1.70.18611370.16782706X-RAY DIFFRACTION100
1.7-1.740.22451430.16682691X-RAY DIFFRACTION100
1.74-1.790.1971270.17332670X-RAY DIFFRACTION100
1.79-1.830.19321480.18162715X-RAY DIFFRACTION99.97
1.83-1.890.20941340.18442680X-RAY DIFFRACTION100
1.89-1.950.19391280.17232690X-RAY DIFFRACTION100
1.95-2.020.22051440.17162704X-RAY DIFFRACTION100
2.02-2.10.21131290.17012713X-RAY DIFFRACTION100
2.1-2.190.18341650.16372677X-RAY DIFFRACTION100
2.19-2.310.21381390.1692689X-RAY DIFFRACTION99.89
2.31-2.450.18541370.16372708X-RAY DIFFRACTION100
2.45-2.640.15841590.1592711X-RAY DIFFRACTION100
2.64-2.90.19761450.15592697X-RAY DIFFRACTION100
2.9-3.320.16231370.1432759X-RAY DIFFRACTION100
3.32-4.150.1581270.12442745X-RAY DIFFRACTION99.97
4.15-12.610.13691480.12722810X-RAY DIFFRACTION99.97

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