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- PDB-9bjq: X-ray crystal structure of wild-type Thermothelomyces thermophilu... -

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Basic information

Entry
Database: PDB / ID: 9bjq
TitleX-ray crystal structure of wild-type 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
ACETATE ION / COPPER (II) ION / OXYGEN MOLECULE / lytic cellulose monooxygenase (C4-dehydrogenating)
Similarity search - Component
Biological speciesThermothelomyces thermophilus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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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)49,21813
Polymers48,5962
Non-polymers62311
Water10,413578
1
A: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5776
Polymers24,2981
Non-polymers2795
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)24,6427
Polymers24,2981
Non-polymers3446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.449, 121.410, 91.909
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
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

21A-708-

HOH

31B-663-

HOH

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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: 24297.832 Da / Num. of mol.: 2
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, 589 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.69 Å3/Da / Density % sol: 54.3 % / Description: 200 mM, 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, 25 % w/v polyethylene glycol 3,350). 1 ul 30 mg/mL 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 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 30 % PEG 3,350. The crystal was subsequently soaked for 5 minutes in well solution with a final concentration of 1 mM CuSO4. 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: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.8→43.77 Å / Num. obs: 51698 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 19.77 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 18.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2985 / CC1/2: 0.87 / Rpim(I) all: 0.258 / Rrim(I) all: 0.668 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.77 Å / SU ML: 0.1549 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.0073
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1859 2011 3.89 %
Rwork0.1553 49653 -
obs0.1565 51505 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 34 578 4040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00673608
X-RAY DIFFRACTIONf_angle_d0.82784933
X-RAY DIFFRACTIONf_chiral_restr0.0597524
X-RAY DIFFRACTIONf_plane_restr0.0065670
X-RAY DIFFRACTIONf_dihedral_angle_d13.71971279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.22851350.19883340X-RAY DIFFRACTION94.38
1.84-1.890.22561410.19023482X-RAY DIFFRACTION98.94
1.89-1.950.21981440.17323531X-RAY DIFFRACTION99.7
1.95-2.010.20611420.16923532X-RAY DIFFRACTION99.89
2.01-2.080.20051430.15883532X-RAY DIFFRACTION99.84
2.08-2.170.18851420.15753537X-RAY DIFFRACTION99.7
2.17-2.260.18481440.15823525X-RAY DIFFRACTION99.4
2.26-2.380.19011440.15763554X-RAY DIFFRACTION99.84
2.38-2.530.21821450.15863563X-RAY DIFFRACTION100
2.53-2.730.19061440.16123553X-RAY DIFFRACTION99.92
2.73-30.19261450.16793574X-RAY DIFFRACTION99.92
3-3.440.18811440.15873594X-RAY DIFFRACTION99.34
3.44-4.330.16831470.13883610X-RAY DIFFRACTION99.52
4.33-39.450.15481510.1363726X-RAY DIFFRACTION99.23

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