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- PDB-7t5e: Neutron structure of Neurospora crassa Polysaccharide Monooxygena... -

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Basic information

Entry
Database: PDB / ID: 7t5e
TitleNeutron structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) low pH vapor exchange
ComponentsLytic polysaccharide monooxygenase
KeywordsOXIDOREDUCTASE / LPMO / monooxygenase / PMO / metalloproteins
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / 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 / lytic cellulose monooxygenase (C4-dehydrogenating)
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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
A: Lytic polysaccharide monooxygenase
B: Lytic polysaccharide monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8986
Polymers46,5982
Non-polymers1,3004
Water6,990388
1
A: 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
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)68.296, 42.269, 70.413
Angle α, β, γ (deg.)90.000, 98.470, 90.000
Int Tables number4
Space group name H-MP1211
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 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.: 2 / Source method: obtained synthetically
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
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 % / 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

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-IDSerial crystal experiment
1295Room temperature1N
2295Room temperature1N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.54
SPALLATION SOURCEORNL Spallation Neutron Source MANDI22-4
Detector
TypeIDDetectorDate
DECTRIS EIGER R 4M1PIXELOct 25, 2018
ORNL ANGER CAMERA2DIFFRACTOMETERJul 17, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
221
341
Reflection

Biso Wilson estimate: 17.17 Å2 / Entry-ID: 7T5E

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRrim(I) allDiffraction-IDNet I/σ(I)
1.9-12.653095097.566.10.9910.11520.1258115.24
2.14-14.651896384.6540.970.15320.1751210.01
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
1.9-1.94.10.2994.428590.880.3443191.75
2.14-2.223.30.3283.0216550.3630.3824274.75

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
Coot0.8.9.2model building
LaueViewdata scaling
Refinement

SU ML: 0.18 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.75 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5TKH

5tkh

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)σ(F)
1.9-12.662X-RAY DIFFRACTION91.1323.52753.760.1820.12750.1303155729391309485.0397.961.34
2.144-14.649NEUTRON DIFFRACTION0.21370.14440.148954187705.0884.980
Refinement stepCycle: final / Resolution: 1.9→12.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 155 1167 4593
Biso mean--47.9 33.12 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01018106
X-RAY DIFFRACTIONf_angle_d1.321813628
X-RAY DIFFRACTIONf_chiral_restr0.0707571
X-RAY DIFFRACTIONf_plane_restr0.00711339
X-RAY DIFFRACTIONf_dihedral_angle_d21.05332075
LS refinement shell

Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1443-2.25690.29891620.20882254NEUTRON DIFFRACTION77
2.2569-2.39780.2791150.19442532NEUTRON DIFFRACTION85
2.3978-2.5820.26911540.17832501NEUTRON DIFFRACTION84
2.582-2.84010.22981250.1572540NEUTRON DIFFRACTION85
2.8401-3.24720.22321230.14692635NEUTRON DIFFRACTION88
3.2472-4.07640.21271390.1352669NEUTRON DIFFRACTION89
4.0764-14.6490.16641360.11742685NEUTRON DIFFRACTION87
1.9-1.96110.25541330.16472476X-RAY DIFFRACTION91
1.9611-2.03090.23361420.15852575X-RAY DIFFRACTION96
2.0309-2.11190.22151260.14782683X-RAY DIFFRACTION98
2.1119-2.20750.18881680.14232661X-RAY DIFFRACTION99
2.2075-2.32320.22241320.1462660X-RAY DIFFRACTION99
2.3232-2.46780.19911430.13892666X-RAY DIFFRACTION99
2.4678-2.65670.2111510.14152696X-RAY DIFFRACTION99
2.6567-2.92110.19831470.13712702X-RAY DIFFRACTION100
2.9211-3.3370.19341350.1322738X-RAY DIFFRACTION99
3.337-4.1790.161320.10182751X-RAY DIFFRACTION99
4.179-12.6620.12081480.10052783X-RAY DIFFRACTION99

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