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- PDB-9z95: Neurospora crassa polysaccharide monooxygenase 9D dose series - p... -

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Basic information

Entry
Database: PDB / ID: 9z95
TitleNeurospora crassa polysaccharide monooxygenase 9D dose series - pseudohelix 17 (5.56 MGy)
ComponentsLytic polysaccharide monooxygenase NCU01050
KeywordsOXIDOREDUCTASE / radiation damage / LPMO / photoreduction / polysaccharide monooxygenase
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / polysaccharide catabolic process / cellulose catabolic process / monooxygenase activity / oxygen binding / copper ion binding / extracellular region
Similarity search - Function
Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
CARBON DIOXIDE / COPPER (II) ION / OXYGEN MOLECULE / DI(HYDROXYETHYL)ETHER / Lytic polysaccharide monooxygenase NCU01050
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMiller, S.A. / O'Dell, W.B. / Meilleur, F.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Dose-dependent structural and electron-density features in the lytic polysaccharide monooxygenase NcAA9D.
Authors: Miller, S.A. / O'Dell, W.B. / Meilleur, F.
History
DepositionNov 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lytic polysaccharide monooxygenase NCU01050
B: Lytic polysaccharide monooxygenase NCU01050
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,50919
Polymers46,5982
Non-polymers1,91117
Water17,132951
1
A: Lytic polysaccharide monooxygenase NCU01050
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,47412
Polymers23,2991
Non-polymers1,17511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lytic polysaccharide monooxygenase NCU01050
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0357
Polymers23,2991
Non-polymers7366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.551, 42.228, 69.562
Angle α, β, γ (deg.)90.000, 98.966, 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

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Protein , 1 types, 2 molecules AB

#1: Protein Lytic polysaccharide monooxygenase NCU01050 / LPMO NCU01050 / Endoglucanase II / LPMO9D / NcLPMO9D / NcPMO-2 / NcPMO2 / Polysaccharide ...LPMO NCU01050 / Endoglucanase II / LPMO9D / NcLPMO9D / NcPMO-2 / NcPMO2 / Polysaccharide monooxygenase 2 / PMO-2 / PMO2 / Type-2 polysaccharide monooxygenase / Type-2 PMO


Mass: 23299.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: gh61-4, NCU01050 / Plasmid: pPICZaA / Production host: Komagataella phaffii (fungus) / Strain (production host): SuperMan5(HIS+)
References: UniProt: Q1K8B6, lytic cellulose monooxygenase (C4-dehydrogenating)

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: 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

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Non-polymers , 6 types, 966 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 951 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.36 % / Description: Elongated cuboid
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 3350, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→44.53 Å / Num. obs: 289779 / % possible obs: 93.95 % / Redundancy: 3.6 % / Biso Wilson estimate: 9.65 Å2 / CC1/2: 0.966 / CC star: 0.991 / Rmerge(I) obs: 0.1137 / Rpim(I) all: 0.08156 / Rrim(I) all: 0.1409 / Net I/σ(I): 5.37
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.3296 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 10308 / CC1/2: 0.877 / CC star: 0.967 / Rpim(I) all: 0.193 / Rrim(I) all: 0.3825 / % possible all: 89.9

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Processing

Software
NameVersionClassification
DIALS3.26data reduction
DIALS3.26data scaling
PHENIX1.21.2_5419phasing
Coot1.1.18model building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→44.53 Å / SU ML: 0.1077 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.8149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.191 3848 1.33 %
Rwork0.1704 285931 -
obs0.1707 289779 93.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.05 Å2
Refinement stepCycle: LAST / Resolution: 1.1→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 119 951 4342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01324122
X-RAY DIFFRACTIONf_angle_d1.2825689
X-RAY DIFFRACTIONf_chiral_restr0.0989638
X-RAY DIFFRACTIONf_plane_restr0.0115763
X-RAY DIFFRACTIONf_dihedral_angle_d12.61591584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.33611420.283510166X-RAY DIFFRACTION89.9
1.11-1.130.2641270.264910287X-RAY DIFFRACTION91.67
1.13-1.140.24971410.248210341X-RAY DIFFRACTION91.32
1.14-1.160.24951370.232310386X-RAY DIFFRACTION92.35
1.16-1.180.24341490.225610375X-RAY DIFFRACTION92.1
1.18-1.20.25011250.214710429X-RAY DIFFRACTION92.56
1.2-1.220.23321460.212910512X-RAY DIFFRACTION92.88
1.22-1.240.25481500.202810361X-RAY DIFFRACTION92.47
1.24-1.260.23911440.204610522X-RAY DIFFRACTION93.72
1.26-1.280.18831330.192810546X-RAY DIFFRACTION93.14
1.28-1.310.21011380.191510657X-RAY DIFFRACTION94.4
1.31-1.340.20671510.181810602X-RAY DIFFRACTION94.32
1.34-1.370.20041380.176610715X-RAY DIFFRACTION94.37
1.37-1.40.22691360.17310672X-RAY DIFFRACTION94.74
1.4-1.440.20921470.165210687X-RAY DIFFRACTION95.38
1.44-1.480.20591460.159110760X-RAY DIFFRACTION95.49
1.48-1.530.15171560.153210804X-RAY DIFFRACTION95.75
1.53-1.590.17261450.148210832X-RAY DIFFRACTION96.06
1.59-1.650.14811460.148310872X-RAY DIFFRACTION96.26
1.65-1.730.17971470.150910841X-RAY DIFFRACTION96.4
1.73-1.820.17631480.151710869X-RAY DIFFRACTION96.34
1.82-1.930.14451500.153910764X-RAY DIFFRACTION95.33
1.93-2.080.17011340.144110705X-RAY DIFFRACTION95.22
2.08-2.290.17231360.155810662X-RAY DIFFRACTION94.6
2.29-2.620.19021480.156810640X-RAY DIFFRACTION94.39
2.62-3.30.18521490.160210554X-RAY DIFFRACTION93.49
3.3-44.530.18561390.172810370X-RAY DIFFRACTION92.1

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