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- PDB-9bjs: X-ray crystal structure of Y62W Thermothelomyces thermophilus pol... -

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Basic information

Entry
Database: PDB / ID: 9bjs
TitleX-ray crystal structure of Y62W 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
ACETIC ACID / COPPER (II) ION / OXYGEN MOLECULE / lytic cellulose monooxygenase (C4-dehydrogenating)
Similarity search - Component
Biological speciesThermothelomyces thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)49,14111
Polymers48,6422
Non-polymers4999
Water8,413467
1
A: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6016
Polymers24,3211
Non-polymers2805
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)24,5415
Polymers24,3211
Non-polymers2204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.692, 122.395, 91.699
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

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Protein , 1 types, 2 molecules AB

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


Mass: 24320.867 Da / Num. of mol.: 2 / Mutation: Y62W
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

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Non-polymers , 5 types, 476 molecules

#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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.71 Å3/Da / Density % sol: 54.7 %
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, 25 % w/v polyethylene glycol 3,350). 1 ul 30 mg/mL Y62W 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, 25 % w/v polyethylene glycol 3,350). 1 ul 30 mg/mL Y62W 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 10 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: 1.00003 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: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→43.79 Å / Num. obs: 38124 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.74 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Net I/σ(I): 14.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 2772 / CC1/2: 0.942 / CC star: 0.98 / Rpim(I) all: 0.175 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.79 Å / SU ML: 0.2141 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.7911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2333 1483 4.05 %
Rwork0.1985 35150 -
obs0.1999 36633 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.18 Å2
Refinement stepCycle: LAST / Resolution: 2→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 26 467 3923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283566
X-RAY DIFFRACTIONf_angle_d0.57294870
X-RAY DIFFRACTIONf_chiral_restr0.0454516
X-RAY DIFFRACTIONf_plane_restr0.0037658
X-RAY DIFFRACTIONf_dihedral_angle_d12.3211247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.29691350.27283161X-RAY DIFFRACTION95.73
2.06-2.140.35191340.30393154X-RAY DIFFRACTION96
2.14-2.220.23161350.21893176X-RAY DIFFRACTION96.67
2.22-2.330.4084970.3342336X-RAY DIFFRACTION70.44
2.33-2.450.24051390.19243294X-RAY DIFFRACTION100
2.45-2.60.19421400.18673300X-RAY DIFFRACTION99.97
2.6-2.80.20411360.19643307X-RAY DIFFRACTION99.57
2.8-3.080.21561400.19043318X-RAY DIFFRACTION99.34
3.08-3.530.21931400.17883321X-RAY DIFFRACTION99.23
3.53-4.450.22011390.17163292X-RAY DIFFRACTION97.33
4.45-43.790.18841480.15643491X-RAY DIFFRACTION99.75

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