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- PDB-6fnd: Crystal structure of Toxoplasma gondii AKMT -

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Basic information

Entry
Database: PDB / ID: 6fnd
TitleCrystal structure of Toxoplasma gondii AKMT
Components(Apical complex lysine ...) x 4
KeywordsTRANSFERASE / Lysine methyltransferase / SET domain / AKMT / homodimer
Function / homology
Function and homology information


methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Apical complex lysine methyltransferase / Apical complex lysine methyltransferase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
Toxoplasma gondii TgCatPRC2 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.101 Å
AuthorsPivovarova, Y. / Dong, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW 1258 Austria
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structure of a Novel Dimeric SET Domain Methyltransferase that Regulates Cell Motility.
Authors: Pivovarova, Y. / Liu, J. / Lesigang, J. / Koldyka, O. / Rauschmeier, R. / Hu, K. / Dong, G.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apical complex lysine methyltransferase
B: Apical complex lysine methyltransferase
C: Apical complex lysine methyltransferase
D: Apical complex lysine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,26247
Polymers193,1124
Non-polymers3,15043
Water7,819434
1
A: Apical complex lysine methyltransferase
B: Apical complex lysine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,83825
Polymers96,1312
Non-polymers1,70723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-51 kcal/mol
Surface area39250 Å2
MethodPISA
2
C: Apical complex lysine methyltransferase
D: Apical complex lysine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,42422
Polymers96,9812
Non-polymers1,44320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-14 kcal/mol
Surface area39310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.935, 89.371, 91.720
Angle α, β, γ (deg.)108.690, 101.310, 103.410
Int Tables number1
Space group name H-MP1

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Components

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Apical complex lysine ... , 4 types, 4 molecules ABCD

#1: Protein Apical complex lysine methyltransferase


Mass: 48315.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGPRC2_216080B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A151H4R7, UniProt: B9Q0K5*PLUS
#2: Protein Apical complex lysine methyltransferase


Mass: 47815.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii TgCatPRC2 (eukaryote)
Gene: TGPRC2_216080B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A151H4R7, UniProt: B9Q0K5*PLUS
#3: Protein Apical complex lysine methyltransferase


Mass: 48413.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii TgCatPRC2 (eukaryote)
Gene: TGPRC2_216080B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A151H4R7, UniProt: B9Q0K5*PLUS
#4: Protein Apical complex lysine methyltransferase


Mass: 48567.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii TgCatPRC2 (eukaryote)
Gene: TGPRC2_216080B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A151H4R7, UniProt: B9Q0K5*PLUS

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Non-polymers , 6 types, 477 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47 % / Description: orthorhombic
Crystal growTemperature: 277 K / Method: evaporation / pH: 9
Details: 0.1 M Tris-HCl (pH 9.0), 0.2 M MgCl2, 30% (w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.28225 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2016
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28225 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 167741 / % possible obs: 82.8 % / Redundancy: 2.8 % / CC1/2: 0.99 / Rrim(I) all: 0.138 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 14053 / CC1/2: 0.79 / Rrim(I) all: 0.967 / % possible all: 43.2

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.101→20.071 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.226 3900 2.33 %
Rwork0.1913 --
obs0.1921 167722 83.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.25 Å2 / Biso mean: 58.194 Å2 / Biso min: 18.7 Å2
Refinement stepCycle: final / Resolution: 2.101→20.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13505 0 172 434 14111
Biso mean--75.69 48.98 -
Num. residues----1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414002
X-RAY DIFFRACTIONf_angle_d0.70218990
X-RAY DIFFRACTIONf_chiral_restr0.0452061
X-RAY DIFFRACTIONf_plane_restr0.0052431
X-RAY DIFFRACTIONf_dihedral_angle_d4.5879816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1007-2.12630.3048590.29052375243434
2.1263-2.15320.3435670.28312785285240
2.1532-2.18140.3171720.27853195326745
2.1814-2.21130.2881820.26553516359850
2.2113-2.24280.2632860.27343936402256
2.2428-2.27630.32321130.26034432454563
2.2763-2.31180.26271200.26355122524273
2.3118-2.34960.34271520.26346444659690
2.3496-2.39010.28931500.24186443659392
2.3901-2.43350.3351750.23326476665193
2.4335-2.48020.23831500.22186671682193
2.4802-2.53070.22921470.23376587673494
2.5307-2.58570.24471490.22266553670293
2.5857-2.64570.26541720.22726539671193
2.6457-2.71170.26891500.23046533668392
2.7117-2.78480.28021550.21826654680994
2.7848-2.86650.26111540.21616573672794
2.8665-2.95880.26781580.21876658681694
2.9588-3.06420.2381670.2216615678294
3.0642-3.18640.25631590.20936526668594
3.1864-3.33080.24911500.20396533668393
3.3308-3.50550.24081580.19026637679595
3.5055-3.72390.2341570.1766691684894
3.7239-4.00930.16621520.16576697684995
4.0093-4.40890.17851650.15036588675394
4.4089-5.0380.18941640.15126714687896
5.038-6.31440.20951490.18146624677394
6.3144-20.07140.18811680.15926705687395
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)
10.1562-0.0390.0591.3840.28730.87540.19380.7569-0.2543-0.4472-0.21750.38970.0698-0.2739-0.05420.42670.047-0.07180.7198-0.08440.3628-15.1147-7.9803-49.5061
20.3205-0.14660.05680.35050.29080.509-0.10940.0243-0.14510.3333-0.1478-0.26670.25470.0117-0.00010.4541-0.00160.06270.39440.01150.327725.4133-32.7122-20.2576
30.05170.0103-0.02340.1579-0.21480.2661-0.16430.507-0.531-0.8412-0.0018-0.37760.9447-0.27370.00690.8389-0.07610.16840.6561-0.12660.67628.0408-48.5334-46.1476
40.65040.0622-0.64760.8599-0.20161.2751-0.1750.0513-0.402-0.21970.0059-0.16960.65660.05730.00060.5420.02750.08130.43050.00860.493129.0415-41.7187-35.7079
50.41280.08460.02380.3807-0.25210.1690.02370.15860.033-0.1692-0.1216-0.3108-0.0175-0.07850.00020.30880.01520.06130.45-0.00670.344427.898-20.6926-38.1835
60.1936-0.034-0.15250.0811-0.07670.1544-0.0299-0.1251-0.3307-0.03880.01230.20040.00170.1042-00.2783-0.00580.04020.348-0.01230.3499.2962-25.6693-32.234
70.2195-0.085-0.0380.3497-0.34190.3622-0.01350.0524-0.6589-0.02360.06310.33550.239-0.03660.01080.3161-0.0083-0.00210.3788-0.06240.4923-6.1663-23.6029-31.8859
80.0337-0.01320.00690.1626-0.18810.1643-0.07710.6686-0.456-0.46560.01830.17180.5088-0.12730.01120.5292-0.0408-0.0290.6375-0.23520.5098-5.0988-24.9854-48.8969
90.20540.2871-0.18930.4252-0.15940.19780.07140.6159-0.1246-0.4176-0.12170.11460.0991-0.02-0.01660.46470.0639-0.01640.6234-0.07650.26396.5021-16.0426-52.0289
100.05150.1052-0.03520.28530.01080.14530.10910.28570.2236-0.2919-0.0372-0.2242-0.2416-0.31720.37450.47540.10470.08820.65420.09970.273715.9252-5.5231-54.9988
110.1314-0.0440.04650.1663-0.05050.06160.03450.05450.1439-0.2425-0.157-0.3606-0.09460.42890.01110.50060.12710.10060.66930.08720.281321.9627-6.8504-58.8515
120.88110.02320.70890.84750.79151.8892-0.4374-0.50491.93120.361-0.67840.3282-0.4711-1.0771-1.06320.75360.0052-0.29740.3439-0.40291.4115-15.454717.39312.5789
130.39110.0327-0.17610.6212-0.00140.2462-0.3081-0.65151.43670.2847-0.12011.3712-0.5228-0.3346-0.21660.4573-0.3109-0.73010.1871-0.54811.9779-7.197416.4016.59
142.5302-0.15410.5621.8442-0.45591.2118-0.4348-0.40130.49810.14020.04620.1246-0.2873-0.0575-0.15310.39890.0404-0.12930.3043-0.07410.38678.1704-3.703214.0839
151.01380.3381-0.32281.1431-0.32112.0132-0.18090.1611-0.2428-0.0736-0.0108-0.54550.45940.68950.00550.52310.10170.17120.5632-0.02550.552637.4367-39.7867-8.4084
160.8516-0.30280.14360.58610.16080.7788-0.15740.21270.1542-0.2611-0.1115-0.3015-0.03080.1807-0.00130.4591-0.06080.02970.36490.10510.409924.9759-16.0884-3.2836
170.7784-0.04950.13190.99510.63750.6282-0.3446-0.24450.2970.0075-0.0929-0.35960.00780.4282-0.00920.3355-0.0071-0.05840.45090.12930.487232.3536-10.458912.3934
181.04420.10770.12240.4828-0.36470.5801-0.1562-0.4819-0.14180.12170.038-0.09090.03560.0750.00220.38240.05050.08130.42160.07670.313316.1105-26.966621.8512
190.68360.03631.12651.18740.2940.9393-0.32810.15310.56580.1898-0.0741-0.3991-0.49070.0118-0.10490.5208-0.0387-0.09170.35120.03770.7329-13.639221.4193-21.1749
201.85180.30940.0851.67940.21861.7273-0.0102-0.11490.56880.0274-0.00970.1232-0.3777-0.0243-0.00930.3198-0.0174-0.00240.2818-0.04540.3286-13.633116.0304-24.501
211.2264-0.2752-0.66471.26060.49110.81870.16050.27130.4469-0.1863-0.1268-0.1978-0.0812-0.11220.00740.2770.02340.06350.34850.08790.31158.18384.2665-42.3347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 638 through 708 )C638 - 708
2X-RAY DIFFRACTION2chain 'D' and (resid 288 through 334 )D288 - 334
3X-RAY DIFFRACTION3chain 'D' and (resid 335 through 374 )D335 - 374
4X-RAY DIFFRACTION4chain 'D' and (resid 375 through 452 )D375 - 452
5X-RAY DIFFRACTION5chain 'D' and (resid 453 through 483 )D453 - 483
6X-RAY DIFFRACTION6chain 'D' and (resid 484 through 521 )D484 - 521
7X-RAY DIFFRACTION7chain 'D' and (resid 522 through 572 )D522 - 572
8X-RAY DIFFRACTION8chain 'D' and (resid 573 through 595 )D573 - 595
9X-RAY DIFFRACTION9chain 'D' and (resid 596 through 658 )D596 - 658
10X-RAY DIFFRACTION10chain 'D' and (resid 659 through 685 )D659 - 685
11X-RAY DIFFRACTION11chain 'D' and (resid 686 through 709 )D686 - 709
12X-RAY DIFFRACTION12chain 'A' and (resid 285 through 411 )A285 - 411
13X-RAY DIFFRACTION13chain 'A' and (resid 412 through 452 )A412 - 452
14X-RAY DIFFRACTION14chain 'A' and (resid 453 through 707 )A453 - 707
15X-RAY DIFFRACTION15chain 'B' and (resid 292 through 462 )B292 - 462
16X-RAY DIFFRACTION16chain 'B' and (resid 463 through 552 )B463 - 552
17X-RAY DIFFRACTION17chain 'B' and (resid 553 through 632 )B553 - 632
18X-RAY DIFFRACTION18chain 'B' and (resid 633 through 709 )B633 - 709
19X-RAY DIFFRACTION19chain 'C' and (resid 289 through 374 )C289 - 374
20X-RAY DIFFRACTION20chain 'C' and (resid 375 through 511 )C375 - 511
21X-RAY DIFFRACTION21chain 'C' and (resid 512 through 637 )C512 - 637

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