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- PDB-6cu3: Crystal structure of a protein arginine N-methyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 6cu3
TitleCrystal structure of a protein arginine N-methyltransferase from Naegleria fowleri
Componentsprotein arginine N-methyltransferase
KeywordsTRANSFERASE / NIAID / structural genomics / SAM / SAH / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


protein-arginine N-methyltransferase activity / histone methyltransferase activity / methylation / nucleus
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Distorted Sandwich ...Methyltransferase domain / Methyltransferase domain / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / : / Arginine methyltransferase oligomerization subdomain / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Distorted Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Mainly Beta
Similarity search - Domain/homology
Protein arginine N-methyltransferase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a protein arginine N-methyltransferase from Naegleria fowleri
Authors: Edwards, T.E. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S.
History
DepositionMar 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein arginine N-methyltransferase
B: protein arginine N-methyltransferase
C: protein arginine N-methyltransferase
D: protein arginine N-methyltransferase
E: protein arginine N-methyltransferase
F: protein arginine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,29924
Polymers232,1826
Non-polymers1,11718
Water8,233457
1
A: protein arginine N-methyltransferase
hetero molecules

A: protein arginine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,01512
Polymers77,3942
Non-polymers62110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4150 Å2
ΔGint-1 kcal/mol
Surface area27030 Å2
MethodPISA
2
B: protein arginine N-methyltransferase
E: protein arginine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,13914
Polymers77,3942
Non-polymers74512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint13 kcal/mol
Surface area27140 Å2
MethodPISA
3
C: protein arginine N-methyltransferase
F: protein arginine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4563
Polymers77,3942
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-22 kcal/mol
Surface area27670 Å2
MethodPISA
4
D: protein arginine N-methyltransferase

D: protein arginine N-methyltransferase


Theoretical massNumber of molelcules
Total (without water)77,3942
Polymers77,3942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2750 Å2
ΔGint-20 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.630, 101.460, 105.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 21 or (resid 22 through 23...
21(chain B and (resid 21 or (resid 22 through 23...
31(chain C and (resid 21 or (resid 22 through 23...
41(chain D and (resid 21 through 22 or (resid 23...
51(chain E and (resid 21 or (resid 22 through 23...
61(chain F and (resid 21 through 26 or resid 28...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 21 or (resid 22 through 23...A21
121(chain A and (resid 21 or (resid 22 through 23...A22 - 23
131(chain A and (resid 21 or (resid 22 through 23...A18 - 328
141(chain A and (resid 21 or (resid 22 through 23...A18 - 328
151(chain A and (resid 21 or (resid 22 through 23...A18 - 328
161(chain A and (resid 21 or (resid 22 through 23...A18 - 328
211(chain B and (resid 21 or (resid 22 through 23...B21
221(chain B and (resid 21 or (resid 22 through 23...B22 - 23
231(chain B and (resid 21 or (resid 22 through 23...B17 - 328
241(chain B and (resid 21 or (resid 22 through 23...B17 - 328
251(chain B and (resid 21 or (resid 22 through 23...B17 - 328
261(chain B and (resid 21 or (resid 22 through 23...B17 - 328
311(chain C and (resid 21 or (resid 22 through 23...C21
321(chain C and (resid 21 or (resid 22 through 23...C22 - 23
331(chain C and (resid 21 or (resid 22 through 23...C19 - 328
341(chain C and (resid 21 or (resid 22 through 23...C19 - 328
351(chain C and (resid 21 or (resid 22 through 23...C19 - 328
361(chain C and (resid 21 or (resid 22 through 23...C19 - 328
411(chain D and (resid 21 through 22 or (resid 23...D21 - 22
421(chain D and (resid 21 through 22 or (resid 23...D23
431(chain D and (resid 21 through 22 or (resid 23...D18 - 328
441(chain D and (resid 21 through 22 or (resid 23...D18 - 328
451(chain D and (resid 21 through 22 or (resid 23...D18 - 328
461(chain D and (resid 21 through 22 or (resid 23...D18 - 328
511(chain E and (resid 21 or (resid 22 through 23...E21
521(chain E and (resid 21 or (resid 22 through 23...E22 - 23
531(chain E and (resid 21 or (resid 22 through 23...E20 - 328
541(chain E and (resid 21 or (resid 22 through 23...E20 - 328
551(chain E and (resid 21 or (resid 22 through 23...E20 - 328
561(chain E and (resid 21 or (resid 22 through 23...E20 - 328
611(chain F and (resid 21 through 26 or resid 28...F21 - 26
621(chain F and (resid 21 through 26 or resid 28...F28 - 46
631(chain F and (resid 21 through 26 or resid 28...F48 - 49
641(chain F and (resid 21 through 26 or resid 28...F51 - 130
651(chain F and (resid 21 through 26 or resid 28...F20 - 328
661(chain F and (resid 21 through 26 or resid 28...F0
671(chain F and (resid 21 through 26 or resid 28...F171
681(chain F and (resid 21 through 26 or resid 28...F20 - 328
691(chain F and (resid 21 through 26 or resid 28...F20 - 328
6101(chain F and (resid 21 through 26 or resid 28...F20 - 328
6111(chain F and (resid 21 through 26 or resid 28...F20 - 328
6121(chain F and (resid 21 through 26 or resid 28...F20 - 328

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Components

#1: Protein
protein arginine N-methyltransferase


Mass: 38696.926 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E135*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5.5 mg/mL NafoA.01523.a.B1.PW37976 against JCSG+ screen condition A3 (0.2 M ammonium citrate, 25% PEG3350), cryoprotectant: 20% ethylene glycol, crystal tracking ID 286783a3, unique puck ID rmz3-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 18, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→46.997 Å / Num. obs: 93675 / % possible obs: 99.9 % / Redundancy: 5.39 % / Biso Wilson estimate: 40.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.085 / Χ2: 1.043 / Net I/σ(I): 16.18 / Num. measured all: 504864 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.565.4850.5583.1137484683768340.8870.616100
2.56-2.645.4850.443.8736735670266970.9330.48699.9
2.64-2.715.4740.3684.6735589650365010.9490.407100
2.71-2.85.4920.3135.4934786633663340.960.345100
2.8-2.895.4760.2576.6833372609960940.9720.28399.9
2.89-2.995.4810.2048.1232602595059480.9820.225100
2.99-3.15.4680.1729.5631189570757040.9870.1999.9
3.1-3.235.4410.12412.6130208555355520.9930.136100
3.23-3.375.4430.115.4328846530253000.9950.11100
3.37-3.545.4090.07918.4527481508650810.9960.08799.9
3.54-3.735.4050.06521.8926116483548320.9980.07199.9
3.73-3.955.350.05525.1424464457745730.9980.0699.9
3.95-4.235.3150.04729.0723068434443400.9990.05299.9
4.23-4.565.2820.04231.6521248402540230.9990.046100
4.56-55.2330.03833.1119488372637240.9990.04399.9
5-5.595.2250.03833.3217760339933990.9990.042100
5.59-6.455.2480.04130.2615748300530010.9990.04699.9
6.45-7.915.2110.03433.9713341256825600.9990.03799.7
7.91-11.184.9970.02639.42101542039203210.02899.7
11.18-46.9974.5240.02340.075185119411460.9990.02696

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3Q7E

3q7e


Resolution: 2.5→46.997 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.64
RfactorNum. reflection% reflection
Rfree0.2327 2166 2.31 %
Rwork0.1898 --
obs0.1908 93624 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.97 Å2 / Biso mean: 54.925 Å2 / Biso min: 17.06 Å2
Refinement stepCycle: final / Resolution: 2.5→46.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14035 0 72 458 14565
Biso mean--69.56 46.86 -
Num. residues----1819
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4410X-RAY DIFFRACTION3.916TORSIONAL
12B4410X-RAY DIFFRACTION3.916TORSIONAL
13C4410X-RAY DIFFRACTION3.916TORSIONAL
14D4410X-RAY DIFFRACTION3.916TORSIONAL
15E4410X-RAY DIFFRACTION3.916TORSIONAL
16F4410X-RAY DIFFRACTION3.916TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.55810.26081320.219160296161100
2.5581-2.62210.30741190.216260336152100
2.6221-2.6930.29261390.223860406179100
2.693-2.77220.32421620.226860386200100
2.7722-2.86170.24961540.214260146168100
2.8617-2.96390.31240.204260536177100
2.9639-3.08260.24961440.209360846228100
3.0826-3.22280.2761490.213960256174100
3.2228-3.39270.20211580.196260766234100
3.3927-3.60520.24311530.195860566209100
3.6052-3.88340.23381600.181861086268100
3.8834-4.2740.2081360.160961226258100
4.274-4.89190.18351360.151561766312100
4.8919-6.16110.21211410.177162186359100
6.1611-47.00480.2171590.20116386654599
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)
11.11770.69621.11521.73280.64271.11130.08080.2388-0.34010.0638-0.06530.15330.3564-0.131-0.12630.678-0.41730.07511.8417-0.71190.9916-60.088332.5094-100.6258
20.2660.32680.11240.98470.69490.57490.01840.6444-0.4249-0.57030.02350.35720.1291-0.2657-0.02850.7886-0.0934-0.27631.9466-0.43670.6504-57.795751.6378-104.3239
30.097-0.3451-0.02011.64490.35240.20480.00160.4638-0.3611-0.2852-0.0052-0.11510.0013-0.7963-0.01450.471-0.040.03470.9876-0.00450.3105-39.602266.2199-87.1495
40.2529-0.58590.00941.4587-0.23120.74560.06731.3601-0.1322-0.367-0.19280.4423-0.0209-1.02430.05620.48050.0721-0.00671.489-0.01190.5224-52.729964.8636-87.8779
50.9596-0.1059-0.23540.377-0.63361.51080.35011.42190.1025-0.5993-0.2680.1455-0.2576-0.32770.10680.67030.3495-0.03951.90620.31570.6288-50.575671.6309-97.5316
61.37471.80540.67333.79970.03032.6892-0.02530.1596-0.1159-0.12560.10180.09980.17230.1903-0.0590.21260.0456-0.00830.2169-0.03620.3522-23.8141-1.9384-52.9991
72.2541-0.8438-1.24561.19360.22530.75270.0479-0.2219-0.04970.03960.1108-0.13890.08430.1111-0.11750.2641-0.0113-0.02010.2648-0.0270.31523.756515.2824-38.4179
83.80931.12971.74743.84531.17052.4582-0.06480.00120.2481-0.0333-0.08410.1327-0.01780.03220.1570.20920.0464-0.00220.17670.00270.246-10.934519.9898-41.582
92.296-1.47111.09334.2749-0.49212.63140.028-0.433-0.32220.16960.16580.06270.1144-0.3315-0.17550.2324-0.0054-0.00410.25830.05520.2986-17.291248.7357-46.2896
104.05-0.37411.2421.8339-0.41791.1186-0.01520.01930.37580.0014-0.0618-0.0825-0.014-0.04710.06370.24230.01430.04070.1761-0.00420.263-33.962369.2548-59.874
111.7508-0.9719-2.03354.2594-0.51854.62-0.03980.4821-0.0101-0.4202-0.0943-0.3330.0681-0.38610.11340.3958-0.09290.12530.5385-0.01960.3726-15.224859.2064-100.0316
120.4471-0.3067-0.36691.69980.11821.6009-0.59790.5264-0.7153-0.4970.0474-0.26190.5259-0.25210.33570.6635-0.17520.32590.6073-0.2250.6455-26.401134.5774-87.8407
131.1067-0.5479-1.57781.7930.18682.50790.212-0.33290.45340.5935-0.26130.5014-0.184-0.0638-0.02060.6537-0.05680.21710.7809-0.34460.7674-22.81688.50190.4279
142.2156-0.2203-0.7762.71440.30871.4756-0.0607-0.2553-0.040.3756-0.18790.19860.0155-0.2140.26110.4071-0.01210.07580.452-0.05910.2651-12.0762-15.7761-11.2989
152.7259-1.5918-1.21834.49490.28522.5495-0.1258-0.31910.11420.20810.22220.1497-0.03480.2447-0.09290.2213-0.01480.0020.21-0.01210.2926-66.267852.6255-50.3138
163.0311.047-0.72631.79290.14330.7874-0.12840.084-0.4482-0.07290.0798-0.17080.05960.05770.03760.2740.00340.03030.1921-0.00090.3648-47.433632.1743-60.4465
170.33030.12310.41531.8640.91121.6325-0.03720.7046-0.52870.0133-0.00140.150.3129-0.28110.02660.6663-0.4326-0.01511.576-0.63011.034-57.126341.3053-89.9937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 37 through 97 )F37 - 97
2X-RAY DIFFRACTION2chain 'F' and (resid 98 through 142 )F98 - 142
3X-RAY DIFFRACTION3chain 'F' and (resid 143 through 182 )F143 - 182
4X-RAY DIFFRACTION4chain 'F' and (resid 183 through 289 )F183 - 289
5X-RAY DIFFRACTION5chain 'F' and (resid 290 through 328 )F290 - 328
6X-RAY DIFFRACTION6chain 'A' and (resid 18 through 152 )A18 - 152
7X-RAY DIFFRACTION7chain 'A' and (resid 153 through 202 )A153 - 202
8X-RAY DIFFRACTION8chain 'A' and (resid 203 through 328 )A203 - 328
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 152 )B17 - 152
10X-RAY DIFFRACTION10chain 'B' and (resid 153 through 328 )B153 - 328
11X-RAY DIFFRACTION11chain 'C' and (resid 19 through 152 )C19 - 152
12X-RAY DIFFRACTION12chain 'C' and (resid 153 through 328 )C153 - 328
13X-RAY DIFFRACTION13chain 'D' and (resid 18 through 152 )D18 - 152
14X-RAY DIFFRACTION14chain 'D' and (resid 153 through 328 )D153 - 328
15X-RAY DIFFRACTION15chain 'E' and (resid 20 through 152 )E20 - 152
16X-RAY DIFFRACTION16chain 'E' and (resid 153 through 328 )E153 - 328
17X-RAY DIFFRACTION17chain 'F' and (resid 20 through 36 )F20 - 36

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