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- PDB-8ft7: Crystal structure of SAH bound protein arginine N-methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 8ft7
TitleCrystal structure of SAH bound protein arginine N-methyltransferase 1 (PRMT1) from Naegleria fowleri
ComponentsPUA domain-containing protein
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


gamma-glutamylcyclotransferase activity / glutathione catabolic process / peptidyl-arginine methylation / protein-arginine N-methyltransferase activity / RNA binding
Similarity search - Function
Glutathione-specific gamma-glutamylcyclotransferase / ChaC-like protein / Gamma-glutamyl cyclotransferase-like superfamily / PUA domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase ...Glutathione-specific gamma-glutamylcyclotransferase / ChaC-like protein / Gamma-glutamyl cyclotransferase-like superfamily / PUA domain / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / PUA-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / PUA domain-containing protein
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorOD030394 United States
CitationJournal: To be published
Title: Crystal structure of SAH bound protein arginine N-methyltransferase 1 (PRMT1) from Naegleria fowleri
Authors: Seibold, S. / Battaile, K.P. / Lovell, S.
History
DepositionJan 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn / Item: _diffrn.ambient_temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUA domain-containing protein
B: PUA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7394
Polymers82,9702
Non-polymers7692
Water1,38777
1
A: PUA domain-containing protein
hetero molecules

A: PUA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7394
Polymers82,9702
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Buried area2800 Å2
ΔGint-22 kcal/mol
Surface area26250 Å2
MethodPISA
2
B: PUA domain-containing protein
hetero molecules

B: PUA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7394
Polymers82,9702
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area2820 Å2
ΔGint-22 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.586, 147.886, 152.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein PUA domain-containing protein


Mass: 41484.957 Da / Num. of mol.: 2 / Fragment: NafoA.20639.a.A2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Gene: FDP41_006519 / Plasmid: NafoA.20639.a.A2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6A5BBK9
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Wizard Cryo H6: 30% PEG 200, 100mM Sodium Acetate pH 4.5, 100mM Sodium Chloride. NafoA.20639.a.A2.PW39094 at 8.5 mg/mL Tray: Steve 11/09/22 well D10, 24 hour soak in 5mM S- ...Details: Wizard Cryo H6: 30% PEG 200, 100mM Sodium Acetate pH 4.5, 100mM Sodium Chloride. NafoA.20639.a.A2.PW39094 at 8.5 mg/mL Tray: Steve 11/09/22 well D10, 24 hour soak in 5mM S-adenosylhomocysteine (SAH), Puck: PSL0710, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 10, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→47.95 Å / Num. obs: 49721 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.016 / Rrim(I) all: 0.06 / Χ2: 1.01 / Net I/σ(I): 21.9 / Num. measured all: 680729
Reflection shellResolution: 2.15→2.22 Å / % possible obs: 100 % / Redundancy: 14.5 % / Rmerge(I) obs: 1.485 / Num. measured all: 61863 / Num. unique obs: 4272 / CC1/2: 0.768 / Rpim(I) all: 0.403 / Rrim(I) all: 1.539 / Χ2: 1.05 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→35.6 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 2558 5.15 %
Rwork0.1886 --
obs0.1906 49668 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 52 77 5073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095119
X-RAY DIFFRACTIONf_angle_d0.9226948
X-RAY DIFFRACTIONf_dihedral_angle_d14.8831843
X-RAY DIFFRACTIONf_chiral_restr0.055774
X-RAY DIFFRACTIONf_plane_restr0.008887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.38961510.30712573X-RAY DIFFRACTION100
2.19-2.240.33251540.272588X-RAY DIFFRACTION100
2.24-2.280.30081740.24962527X-RAY DIFFRACTION100
2.28-2.340.2921450.24142593X-RAY DIFFRACTION100
2.34-2.40.31031540.23562583X-RAY DIFFRACTION100
2.4-2.460.24951330.22622596X-RAY DIFFRACTION100
2.46-2.530.32351270.22732630X-RAY DIFFRACTION100
2.53-2.620.27121440.22942567X-RAY DIFFRACTION100
2.62-2.710.27351220.24022624X-RAY DIFFRACTION100
2.71-2.820.33041200.26212636X-RAY DIFFRACTION100
2.82-2.950.30731430.25452580X-RAY DIFFRACTION100
2.95-3.10.3311270.23452641X-RAY DIFFRACTION100
3.1-3.290.26781360.22282628X-RAY DIFFRACTION100
3.29-3.550.27291330.21532633X-RAY DIFFRACTION100
3.55-3.910.20581390.18212648X-RAY DIFFRACTION100
3.91-4.470.19551520.14752644X-RAY DIFFRACTION100
4.47-5.630.16661620.13772653X-RAY DIFFRACTION100
5.63-35.60.18271420.16072766X-RAY DIFFRACTION99

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