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

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Basic information

Entry
Database: PDB / ID: 9zaf
TitleNeurospora crassa polysaccharide monooxygenase 9D dose series - pseudohelix 32 (6.99 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionNov 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)67.540, 42.212, 69.523
Angle α, β, γ (deg.)90.000, 98.952, 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→44.52 Å / Num. obs: 287011 / % possible obs: 93.15 % / Redundancy: 3.6 % / Biso Wilson estimate: 9.84 Å2 / CC1/2: 0.954 / CC star: 0.988 / Rmerge(I) obs: 0.1162 / Rpim(I) all: 0.08413 / Rrim(I) all: 0.1444 / Net I/σ(I): 5.45
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.3467 / Mean I/σ(I) obs: 0.88 / Num. unique obs: 10222 / CC1/2: 0.839 / CC star: 0.955 / Rpim(I) all: 0.2032 / Rrim(I) all: 0.4024 / % possible all: 88.9

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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→44.52 Å / SU ML: 0.1283 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.4378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2084 3803 1.33 %
Rwork0.1801 283208 -
obs0.1805 287011 93.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.21 Å2
Refinement stepCycle: LAST / Resolution: 1.1→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 119 951 4342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00444122
X-RAY DIFFRACTIONf_angle_d0.85475689
X-RAY DIFFRACTIONf_chiral_restr0.0731638
X-RAY DIFFRACTIONf_plane_restr0.0061763
X-RAY DIFFRACTIONf_dihedral_angle_d12.37721584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.25171380.296310084X-RAY DIFFRACTION88.9
1.11-1.130.35671230.277210144X-RAY DIFFRACTION90.59
1.13-1.140.28841540.255410211X-RAY DIFFRACTION90.43
1.14-1.160.25991160.23610267X-RAY DIFFRACTION91.21
1.16-1.180.31621390.227910242X-RAY DIFFRACTION90.98
1.18-1.20.25741420.21910337X-RAY DIFFRACTION91.78
1.2-1.220.22861440.210910361X-RAY DIFFRACTION91.92
1.22-1.240.25151480.208810302X-RAY DIFFRACTION91.75
1.24-1.260.23591360.207410409X-RAY DIFFRACTION92.77
1.26-1.280.20971420.198510411X-RAY DIFFRACTION92.29
1.28-1.310.23871390.198710546X-RAY DIFFRACTION93.34
1.31-1.340.22661370.193110438X-RAY DIFFRACTION93.39
1.34-1.370.22231520.187810601X-RAY DIFFRACTION93.43
1.37-1.40.2171370.182110564X-RAY DIFFRACTION93.88
1.4-1.440.20371460.17610587X-RAY DIFFRACTION94.52
1.44-1.480.20741610.166910613X-RAY DIFFRACTION94.53
1.48-1.530.18521410.160110737X-RAY DIFFRACTION94.86
1.53-1.590.2181370.161710734X-RAY DIFFRACTION95.18
1.59-1.650.22361360.157810712X-RAY DIFFRACTION95.3
1.65-1.730.19691560.162110761X-RAY DIFFRACTION95.47
1.73-1.820.18331400.161610731X-RAY DIFFRACTION95.28
1.82-1.930.17661500.16310660X-RAY DIFFRACTION94.58
1.93-2.080.181310.154610602X-RAY DIFFRACTION94.5
2.08-2.290.15831420.167810611X-RAY DIFFRACTION94.27
2.29-2.620.20011450.170610640X-RAY DIFFRACTION94.35
2.62-3.30.19141410.170210553X-RAY DIFFRACTION93.53
3.3-44.520.21911300.184110350X-RAY DIFFRACTION91.98

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