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- PDB-8dur: Crystal structure of apo protein arginine N-methyltransferase 1 (... -

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Basic information

Entry
Database: PDB / ID: 8dur
TitleCrystal structure of apo protein arginine N-methyltransferase 1 (PRMT1) from Naegleria fowleri
ComponentsProtein arginine N-methyltransferase 1 (PRMT1)
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
PUA domain-containing protein
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 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)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of apo protein arginine N-methyltransferase 1 (PRMT1) from Naegleria fowleri
Authors: Seibold, S. / Liu, L. / Battaile, K.P. / Lovell, S.
History
DepositionJul 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Data collection / Category: 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: Protein arginine N-methyltransferase 1 (PRMT1)
B: Protein arginine N-methyltransferase 1 (PRMT1)


Theoretical massNumber of molelcules
Total (without water)82,9702
Polymers82,9702
Non-polymers00
Water2,396133
1
A: Protein arginine N-methyltransferase 1 (PRMT1)

A: Protein arginine N-methyltransferase 1 (PRMT1)


Theoretical massNumber of molelcules
Total (without water)82,9702
Polymers82,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Buried area2750 Å2
ΔGint-21 kcal/mol
Surface area26770 Å2
MethodPISA
2
B: Protein arginine N-methyltransferase 1 (PRMT1)

B: Protein arginine N-methyltransferase 1 (PRMT1)


Theoretical massNumber of molelcules
Total (without water)82,9702
Polymers82,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area3940 Å2
ΔGint-20 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.501, 147.708, 150.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Protein arginine N-methyltransferase 1 (PRMT1)


Mass: 41484.957 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Gene: FDP41_006519 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6A5BBK9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 54.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Berkeley D8: 100mM MES pH 5.5, 100 mM Ammonium Citrate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-propanol. NafoA.20639.a.A2.PW39094 at 8.5 mg/mL Tray: Original crystals from plate 12655, well ...Details: Berkeley D8: 100mM MES pH 5.5, 100 mM Ammonium Citrate dibasic, 20% (w/v) PEG 3350, 5% (v/v) 2-propanol. NafoA.20639.a.A2.PW39094 at 8.5 mg/mL Tray: Original crystals from plate 12655, well D8 drop 1, reproduced these crystals in a Clover Jr. plate (Rigaku reagents), Puck: PSL1001, Cryo: 80% (v/v) crystallant + 20% (v/v) ethylene glycol

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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: Jun 7, 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: 1.97→47.42 Å / Num. obs: 63443 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 42.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Net I/σ(I): 18.6 / Num. measured all: 455633 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.97-2.026.80.8873017544210.7280.3650.962.2100
9.03-47.426.40.02647257380.9990.0110.02854.198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.8data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CU3

6cu3


Resolution: 1.97→35.48 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3212 5.07 %Random
Rwork0.1956 ---
obs0.1969 63406 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 48.07 Å2
Refinement stepCycle: final / Resolution: 1.97→35.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 0 133 5113
Biso mean---46.63 -
Num. residues----634
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-20.29611320.280825752707100
2-2.030.28711550.272525932748100
2.03-2.060.24321350.246925832718100
2.06-2.10.2551470.240825832730100
2.1-2.140.27291290.237826082737100
2.14-2.180.29561500.226426042754100
2.18-2.220.25491630.23125482711100
2.22-2.270.26561570.216625812738100
2.27-2.320.25231220.216925962718100
2.32-2.380.25231410.222126012742100
2.38-2.450.291170.221926592776100
2.45-2.520.29021340.231625802714100
2.52-2.60.29531470.227426142761100
2.6-2.690.3021240.223626292753100
2.69-2.80.26161430.230726152758100
2.8-2.930.25961430.234426052748100
2.93-3.080.2221460.219326222768100
3.08-3.280.23971640.208825942758100
3.28-3.530.24331370.19952631276899
3.53-3.880.23821240.17912635275999
3.88-4.440.17631230.160526742797100
4.44-5.60.2061290.158626932822100
5.6-35.480.14861500.17412771292199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.25372.43491.36793.81440.7434.65650.05140.0337-0.0771-0.08640.1172-0.17130.31350.1236-0.13240.31030.0592-0.00090.2427-0.03960.3322-16.243-17.689440.2124
20.9942-0.7529-0.40351.56310.47560.38850.07560.0858-0.19440.0874-0.12750.21080.0802-0.0090.04950.3140.0308-0.01810.3376-0.01540.3316-17.7354-43.962734.6442
31.3631-0.4821-1.63241.69680.76455.73270.0470.01760.1344-0.0640.0065-0.0653-0.2043-0.059-0.05390.31410.0001-0.02390.2809-0.02430.3368-1.00054.232814.6124
41.41090.34930.82940.2650.420.93840.0261-0.0435-0.0618-0.03460.07130.0139-0.1616-0.0174-0.09680.37650.0120.00070.3758-0.00790.3453-3.8815-5.6809-12.456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 103 )A15 - 103
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 328 )A104 - 328
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 152 )B9 - 152
4X-RAY DIFFRACTION4chain 'B' and (resid 153 through 328 )B153 - 328

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