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- PDB-9bjt: X-ray crystal structure of Y62F Thermothelomyces thermophilus pol... -

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Basic information

Entry
Database: PDB / ID: 9bjt
TitleX-ray crystal structure of Y62F Thermothelomyces thermophilus polysaccharide monooxygenase 9E
ComponentsGlycoside hydrolase family 61 protein
KeywordsOXIDOREDUCTASE / polysaccharide monooxygenase
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / hydrolase 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 / OXYGEN MOLECULE / lytic cellulose monooxygenase (C4-dehydrogenating)
Similarity search - Component
Biological speciesThermothelomyces thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsThomas, W.C. / Sayler, R.I. / Marletta, M.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM143897 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM149060 United States
National Science Foundation (NSF, United States)CHE-1904540 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Electron transfer in polysaccharide monooxygenase catalysis.
Authors: Sayler, R.I. / Thomas, W.C. / Rose, A.J. / Marletta, M.A.
History
DepositionApr 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 61 protein
B: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7856
Polymers48,5642
Non-polymers2214
Water41423
1
A: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4394
Polymers24,2821
Non-polymers1583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3452
Polymers24,2821
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.894, 114.606, 91.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Glycoside hydrolase family 61 protein / Lytic polysaccharide monooxygenase


Mass: 24281.832 Da / Num. of mol.: 2 / Mutation: Y62F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothelomyces thermophilus (fungus) / Gene: MYCTH_79765 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD 1163 / References: UniProt: G2Q7A5
#2: 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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.74 Å3/Da / Density % sol: 55.1 % / Description: Plate-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The crystal was grown by hanging drop in conditions optimized from Hampton Index HT G8 (0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 28 % w/v polyethylene glycol 3,350). 1 ul 28 mg/mL Y62F Mt ...Details: The crystal was grown by hanging drop in conditions optimized from Hampton Index HT G8 (0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 28 % w/v polyethylene glycol 3,350). 1 ul 28 mg/mL Y62F Mt PMO9E in 50 mM MOPS, 50 mM MES was mixed with 1 uL with 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, and 26% PEG 3,350. The crystal was then cryoprotected for 6 seconds in well solution mixed with cryoprotectants to a final concentration of 8% w/v sucrose, 2% w/v glucose, 8% v/v glycerol, and 8% ethylene glycol
PH range: 7-7.5 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 3→39.51 Å / Num. obs: 11339 / % possible obs: 90.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 15.08 Å2 / CC1/2: 0.839 / CC star: 0.341 / Rmerge(I) obs: 0.341 / Rpim(I) all: 0.205 / Net I/σ(I): 3.1
Reflection shellResolution: 3→3.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1779 / CC1/2: 0.68 / CC star: 0.911 / Rpim(I) all: 0.344 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→39.51 Å / SU ML: 0.3619 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.3162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 1136 10.02 %
Rwork0.2263 10203 -
obs0.2299 11339 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.28 Å2
Refinement stepCycle: LAST / Resolution: 3→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 8 23 3457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793531
X-RAY DIFFRACTIONf_angle_d1.09324825
X-RAY DIFFRACTIONf_chiral_restr0.0541515
X-RAY DIFFRACTIONf_plane_restr0.0061652
X-RAY DIFFRACTIONf_dihedral_angle_d14.14381238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.29621340.24641270X-RAY DIFFRACTION97.5
3.14-3.30.2681480.23211260X-RAY DIFFRACTION98.95
3.3-3.510.27561360.22571224X-RAY DIFFRACTION94.77
3.51-3.780.29551380.25311258X-RAY DIFFRACTION96.28
3.78-4.160.27851480.23931268X-RAY DIFFRACTION97.19
4.16-4.760.22181410.19221287X-RAY DIFFRACTION99.24
4.76-5.990.22741460.20711309X-RAY DIFFRACTION98.18
5.99-39.510.25851450.2291327X-RAY DIFFRACTION95.4

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