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- PDB-6cu5: Crystal structure of a protein arginine N-methyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 6cu5
TitleCrystal structure of a protein arginine N-methyltransferase from Naegleria fowleri bound to SAH
Componentsprotein arginine N-methyltransferase
KeywordsTRANSFERASE / NIAID / structural genomics / brain eating amoeba / Primary Amebic Meningoencephalitis (PAM) / Amebic Encephalitis / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


peptidyl-arginine methylation / protein-arginine N-methyltransferase activity
Similarity search - Function
Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Methyltransferase domain 25 / 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
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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 bound to SAH
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1634
Polymers77,3942
Non-polymers7692
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-22 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.200, 101.450, 80.680
Angle α, β, γ (deg.)90.000, 100.100, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 16 through 38 or (resid 39...
21(chain B and (resid 16 through 143 or (resid 144...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASNASN(chain A and (resid 16 through 38 or (resid 39...AA16 - 3824 - 46
12LYSLYSLYSLYS(chain A and (resid 16 through 38 or (resid 39...AA3947
13THRTHRARGARG(chain A and (resid 16 through 38 or (resid 39...AA15 - 32823 - 336
14THRTHRARGARG(chain A and (resid 16 through 38 or (resid 39...AA15 - 32823 - 336
15THRTHRARGARG(chain A and (resid 16 through 38 or (resid 39...AA15 - 32823 - 336
16THRTHRARGARG(chain A and (resid 16 through 38 or (resid 39...AA15 - 32823 - 336
21GLYGLYLEULEU(chain B and (resid 16 through 143 or (resid 144...BB16 - 14324 - 151
22ARGARGARGARG(chain B and (resid 16 through 143 or (resid 144...BB144152
23GLYGLYARGARG(chain B and (resid 16 through 143 or (resid 144...BB16 - 32824 - 336
24GLYGLYARGARG(chain B and (resid 16 through 143 or (resid 144...BB16 - 32824 - 336
25GLYGLYARGARG(chain B and (resid 16 through 143 or (resid 144...BB16 - 32824 - 336
26GLYGLYARGARG(chain B and (resid 16 through 143 or (resid 144...BB16 - 32824 - 336

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Components

#1: Protein protein arginine N-methyltransferase


Mass: 38696.926 Da / Num. of mol.: 2
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5.5 mg/mL NafoA.01523.a.B1.PW37976 against ProPlex screen condition F12 (1.5 M ammonium sulfate, 0.1 M sodium HEPES, pH 7.0), cryoprotectant: 20% ethylene glycol, crystal tracking ID ...Details: 5.5 mg/mL NafoA.01523.a.B1.PW37976 against ProPlex screen condition F12 (1.5 M ammonium sulfate, 0.1 M sodium HEPES, pH 7.0), cryoprotectant: 20% ethylene glycol, crystal tracking ID 297887f12, unique puck ID bsj2-10

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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: Mar 1, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→42.751 Å / Num. obs: 18861 / % possible obs: 99.9 % / Redundancy: 4.256 % / Biso Wilson estimate: 38.64 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.134 / Χ2: 0.923 / Net I/σ(I): 9.41 / Num. measured all: 80274 / Scaling rejects: 10
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
2.7-2.774.3050.5612.795837135413560.8850.64100
2.77-2.854.2890.5133.015794135313510.8970.58699.9
2.85-2.934.2690.4123.595643132613220.9310.47199.7
2.93-3.024.2760.3364.355443127212730.9510.383100
3.02-3.124.2740.3074.745317124912440.960.35199.6
3.12-3.234.2990.2166.195167120112020.9820.247100
3.23-3.354.2630.1827.084996117911720.9840.20999.4
3.35-3.494.2830.1398.874720109811020.990.16100
3.49-3.644.2470.1219.534595108610820.9920.13999.6
3.64-3.824.3020.10610.774354101310120.9940.12299.9
3.82-4.024.2230.08812.3941899949920.9950.10199.8
4.02-4.274.2540.07114.5739269209230.9970.081100
4.27-4.564.2830.07115.3136588598540.9960.08199.4
4.56-4.934.2370.06516.3334538148150.9930.075100
4.93-5.44.2230.06815.8832187627620.9960.078100
5.4-6.044.2510.07115.2928406666680.9960.081100
6.04-6.974.2070.06815.6225166005980.9970.07899.7
6.97-8.544.1870.06118.2921485145130.9960.07199.8
8.54-12.074.1110.05821.9616283983960.9950.06699.5
12.07-42.7513.7140.05822.118322302240.9950.06797.4

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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 6CU3

6cu3


Resolution: 2.7→42.751 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2658 1868 9.93 %
Rwork0.1884 16938 -
obs0.196 18806 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.67 Å2 / Biso mean: 45.8796 Å2 / Biso min: 11.31 Å2
Refinement stepCycle: final / Resolution: 2.7→42.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4908 0 52 73 5033
Biso mean--39.31 31.25 -
Num. residues----627
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1916X-RAY DIFFRACTION4.309TORSIONAL
12B1916X-RAY DIFFRACTION4.309TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6999-2.77290.37411430.25112661409100
2.7729-2.85450.37171450.273612901435100
2.8545-2.94660.35831490.253512871436100
2.9466-3.05190.3491430.248113151458100
3.0519-3.1740.34271280.245412981426100
3.174-3.31840.33241320.2341325145799
3.3184-3.49330.28821580.199312811439100
3.4933-3.71210.2961320.197613181450100
3.7121-3.99850.25551480.179213011449100
3.9985-4.40050.21541340.142513191453100
4.4005-5.03640.19831620.1412881450100
5.0364-6.3420.20371410.157813291470100
6.342-42.75650.21261530.15871321147499
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)
12.20211.12350.82753.24881.32110.58-0.08230.11380.0053-0.20940.02890.0761-0.18690.04540.04980.50220.014-0.09980.2192-0.00290.218117.98552.636441.8478
2-0.0461-0.15880.7827-0.0856-0.76256.34520.15370.1697-0.1263-0.3540.11550.06880.1349-0.2229-0.09580.7242-0.0232-0.09720.3024-0.03160.3717-4.8045-14.598819.9424
32.03450.81870.28252.8564-0.00920.11810.064-0.07-0.04140.0893-0.0322-0.11870.0401-0.0515-0.02840.3945-0.02-0.08130.22580.02480.18173.2486-19.291332.9904
41.5718-0.1914-0.00732.56421.28060.62060.0128-0.01-0.0727-0.207-0.04120.02660.07680.0534-0.01450.8522-0.0535-0.16970.33310.01780.34930.9617-0.7439-4.0625
50.11590.3660.43150.7592-0.773.6733-0.06160.02870.1228-0.14860.0840.16480.0174-0.3083-0.08340.69170.0369-0.20240.35830.0150.42-3.200619.885519.2714
61.334-0.19620.53522.86650.76722.24780.01840.07320.0044-0.0682-0.0596-0.0079-0.3732-0.18420.040.66930.0344-0.13220.31050.02970.2933-3.335620.012913.2509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 152 )A15 - 152
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 202 )A153 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 328 )A203 - 328
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 152 )B16 - 152
5X-RAY DIFFRACTION5chain 'B' and (resid 153 through 241 )B153 - 241
6X-RAY DIFFRACTION6chain 'B' and (resid 242 through 328 )B242 - 328

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