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- PDB-4ggn: Malaria invasion machinery protein complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4ggn
TitleMalaria invasion machinery protein complex
Components
  • Myosin A tail domain interacting protein MTIP
  • Myosin-A
KeywordsPROTEIN BINDING / Malaria invasion machinery protein / MTIP / MYOA / MYOSIN A-TAIL / MYOA-TAIL INTERACTING PROTEIN
Function / homology
Function and homology information


myosin complex / cytoskeletal motor activity / actin binding / calcium ion binding / ATP binding / plasma membrane
Similarity search - Function
Class XIV myosin, motor domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain ...Class XIV myosin, motor domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myosin A tail domain interacting protein MTIP / Myosin A tail domain interacting protein MTIP / Myosin-A
Similarity search - Component
Biological speciesPlasmodium knowlesi (eukaryote)
Plasmodium yoelii yoelii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKhamrui, S. / Turley, S. / Bergman, L.W. / Hol, W.G.J.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2013
Title: The structure of the D3 domain of Plasmodium falciparum myosin tail interacting protein MTIP in complex with a nanobody.
Authors: Khamrui, S. / Turley, S. / Pardon, E. / Steyaert, J. / Fan, E. / Verlinde, C.L. / Bergman, L.W. / Hol, W.G.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Atomic model
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin A tail domain interacting protein MTIP
B: Myosin A tail domain interacting protein MTIP
C: Myosin A tail domain interacting protein MTIP
D: Myosin-A
E: Myosin-A
F: Myosin-A


Theoretical massNumber of molelcules
Total (without water)49,4006
Polymers49,4006
Non-polymers00
Water3,441191
1
A: Myosin A tail domain interacting protein MTIP
D: Myosin-A


Theoretical massNumber of molelcules
Total (without water)16,4672
Polymers16,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-10 kcal/mol
Surface area7780 Å2
MethodPISA
2
B: Myosin A tail domain interacting protein MTIP
E: Myosin-A


Theoretical massNumber of molelcules
Total (without water)16,4672
Polymers16,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-14 kcal/mol
Surface area8080 Å2
MethodPISA
3
C: Myosin A tail domain interacting protein MTIP
F: Myosin-A


Theoretical massNumber of molelcules
Total (without water)16,4672
Polymers16,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-14 kcal/mol
Surface area7990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.560, 83.403, 84.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myosin A tail domain interacting protein MTIP


Mass: 14665.288 Da / Num. of mol.: 3 / Fragment: D2-D3 domain (unp residues 79-205)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium knowlesi (eukaryote) / Strain: H / Gene: PKH_146380 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: B3LDA6, UniProt: A0A384KCF1*PLUS
#2: Protein/peptide Myosin-A


Mass: 1801.254 Da / Num. of mol.: 3 / Fragment: Myosin tail helix (unp residues 803-817)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii yoelii (eukaryote) / Gene: PY01232 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7RQ71
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, 10% PEG6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.29→41.7 Å / Num. all: 1 / Num. obs: 26831 / % possible obs: 99.34 %
Reflection shellResolution: 2.29→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 23.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→41.7 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.895 / SU B: 14.974 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27942 1338 5 %RANDOM
Rwork0.22577 ---
obs0.22836 25424 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.848 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.29→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 0 191 3611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023467
X-RAY DIFFRACTIONr_bond_other_d0.0020.023263
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.9544646
X-RAY DIFFRACTIONr_angle_other_deg0.7933.0027421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5015416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64324.807181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06715670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2381523
X-RAY DIFFRACTIONr_chiral_restr0.070.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02797
LS refinement shellResolution: 2.287→2.346 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 89 -
Rwork0.292 1592 -
obs--93.34 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
19.69988.44080.77711.37384.18533.1232-0.29621.02020.3691-1.89840.25620.1936-1.4379-0.55270.04011.34870.3163-0.25070.54390.15990.4099-23.778733.8065-40.8683
211.2495-5.7788-1.78828.28783.81894.65490.181.09490.2021-1.4107-0.57670.3255-0.9828-0.36410.39670.85530.1-0.12110.22760.05970.1135-20.851424.6507-39.8646
37.3949-0.58981.25494.62293.78667.9486-0.04760.2044-0.4683-0.7176-0.10610.3771-0.618-0.42910.15370.32930.066-0.09190.1734-0.01620.1105-21.746816.4134-34.439
411.9564-3.87370.673111.86721.58444.6273-0.53650.7333-0.394-1.191-0.18310.9836-1.1555-0.23790.71960.66080.2944-0.31580.6269-0.17350.3008-30.935118.4466-40.4841
50.8116-0.57740.183120.3368-1.38248.4520.1429-0.00910.3569-0.6157-0.13170.8284-1.2954-0.8093-0.01120.73430.3287-0.21330.4418-0.04040.3657-29.279825.9463-34.1403
64.6607-1.0231-2.6216.01661.11225.5349-0.15560.0604-0.0564-0.6936-0.22840.1389-0.0677-0.35320.3840.16010.036-0.05180.1315-0.01230.1429-20.5216.9273-25.1279
717.6198-3.01887.263838.1397.491814.8129-0.405-0.9052-0.50410.3596-0.02890.47250.2732-0.52240.4340.04270.01710.07740.28290.1270.1996-10.59018.1613-22.0753
813.3518-4.8481-6.589212.2113-5.212814.8988-0.5556-0.1156-1.6008-0.1543-0.2050.67161.1459-0.03380.76060.2468-0.00740.12680.27160.03380.3884-8.27831.2254-27.2431
928.1856-10.533322.389412.4009-17.746728.18421.3723-0.2417-1.1925-1.0016-0.9669-0.03011.66281.0424-0.40540.55910.29490.17760.710.23990.6556-1.396-2.8384-24.5254
106.9011-0.71550.43773.1266-3.38197.5039-0.1731-0.0790.0868-0.1106-0.1239-0.16540.15510.72470.2970.1662-0.01550.11210.33440.05420.28370.6634.1074-32.6486
114.5662-0.33683.32061.95411.99695.108-0.02380.0934-0.2460.0467-0.12210.20650.0515-0.18610.14590.1814-0.04870.06120.2354-0.03910.2368-9.59735.834-38.622
1223.5866-9.854514.917619.6849-7.143718.80770.00290.57850.4349-1.0711-0.5427-0.7025-0.81671.31610.53980.3093-0.18760.13630.28550.03220.2226-2.267412.2686-41.5715
135.3103-4.5448-0.14314.71080.461213.0291-0.3044-0.13840.1366-0.10870.1857-0.1355-1.24421.04110.11880.3625-0.26830.01750.44840.08260.2292.917414.7878-32.6406
1426.670.3006-17.2332.6481-1.289918.9931-0.157-0.67110.1335-0.11540.1348-0.7512-0.33161.42240.02210.1095-0.05430.05480.47040.07770.29653.32637.2891-26.0765
155.01193.00531.33672.72833.62838.9870.0971-0.1877-0.0363-0.2550.0396-0.0771-0.88930.3369-0.13670.2369-0.0656-0.01160.3212-0.00110.2678-5.36715.7528-24.9616
168.42046.0646-3.616423.42224.78664.43160.8628-0.41320.78060.1461-0.74911.7228-0.75540.0265-0.11371.01820.4522-0.24490.3413-0.10390.7382-30.554640.4743-19.7109
176.4142-1.69323.178310.1233-3.5456.80160.05120.29170.9638-0.9311-0.54080.093-1.54740.10340.48960.84350.1022-0.09510.1348-0.01690.3593-21.729843.5382-21.7989
189.38440.53015.13925.89961.41519.09720.1693-0.32080.5323-0.673-0.03960.306-0.6242-0.1575-0.12970.22270.03-0.01210.1239-0.030.1989-20.47932.6512-15.4218
1915.06294.865916.80134.86465.226418.7546-0.26141.076-0.0211-2.08850.2425-0.7289-0.1761.23080.01891.24280.0130.36560.39480.04330.4702-10.19135.6837-22.9814
207.14660.43190.51626.96860.30574.2030.02780.4010.5801-1.5955-0.1261-0.0906-1.08710.23080.09830.94840.1297-0.00540.13070.08980.2031-19.341938.7042-28.755
213.15931.7989-3.94526.98671.18995.47580.11550.0423-0.1623-0.6495-0.0565-0.8189-0.2420.1168-0.0590.44320.0664-0.09280.3753-0.14740.3211-17.873128.8067-23.4362
223.13066.527512.547814.367827.375452.2690.21590.1897-0.31810.38890.03750.03750.98870.5725-0.25340.80340.2199-0.22470.4780.04170.8598-10.166320.8169-14.7632
2313.872715.804911.59618.877212.025212.98870.1320.7283-0.864-0.48850.7471-1.37160.88731.2996-0.8790.48370.08960.14940.4109-0.13680.6243-1.811923.654-8.2388
247.4938.28636.928785.6038-9.946410.4680.43410.9662-1.33170.33230.7382-1.54150.31790.9744-1.17230.27470.17930.00960.7084-0.35820.76625.463226.1426-2.1212
2510.36272.18956.21631.4091-1.04999.63280.3195-0.4434-1.328-0.0641-0.1649-0.52930.5328-0.1094-0.15460.72950.012-0.2040.3897-0.1060.61150.004124.66854.263
261.3331-0.32993.37246.9521.48610.4687-0.0406-0.08190.19090.14230.3663-0.8724-0.20810.3776-0.32570.0277-0.05440.05820.3344-0.15190.4683-1.977936.0454-3.6451
2725.7324-0.0320.647425.1783-12.041836.6538-0.1928-0.88781.98460.86560.10370.6204-0.9723-0.98710.08910.05250.02010.04760.2431-0.1190.3682-9.902840.8833-2.8504
280.8146-2.6851-0.286620.1588-1.32383.1272-0.1564-0.47120.04930.44460.37340.17410.4912-0.6476-0.2170.2115-0.1220.00510.828-0.03610.324-12.276432.273.3036
2915.532-5.1186-8.6188.50179.571111.49370.3388-0.6752-0.39122.00750.1521-0.50141.91640.1703-0.49090.6674-0.0546-0.22420.38080.11140.3049-5.65524.22944.269
3011.7343-9.5487.68288.7188-1.120734.42340.3543-0.2522-0.98560.20520.0290.78442.1913-1.0985-0.38330.422-0.1738-0.1060.27110.02860.4248-12.918123.421-4.9834
3128.8204-31.2227-12.236536.433316.41149.0180.53011.4961-0.6093-0.9321-0.55220.4273-0.74980.56570.02210.68670.1301-0.25280.7423-0.02240.4863-38.967524.3369-31.169
3222.8875-20.9531-3.340919.2192.99360.60970.1330.1392-1.0405-0.1312-0.04221.08710.0153-0.2085-0.09080.40410.1646-0.22840.59310.09330.7333-44.257927.9081-24.58
332.82920.15121.71126.17-3.42034.49420.006-0.08170.10270.4232-0.04240.707-0.3707-0.72520.03640.21440.1304-0.09890.432-0.14850.3523-37.903619.667-20.0606
344.1649-1.4939-0.72047.08562.24324.4477-0.093-0.21220.30390.0675-0.15490.3386-0.4741-0.4620.24790.13710.1391-0.11680.2284-0.07330.2742-32.37721.8532-14.6013
355.5497-0.4357-0.98941.27810.54066.0362-0.16990.00150.4298-0.3428-0.02610.3662-0.5476-0.46960.19610.28270.2128-0.19040.2414-0.08250.398-36.171530.712-19.9447
365.33690.34550.34372.68762.68632.68990.0276-0.18570.2661-0.3368-0.13350.1385-0.3314-0.1440.10590.20080.1284-0.13520.2008-0.04030.27-27.515524.3215-18.1991
374.34672.89521.970523.6075-14.162415.37260.2348-0.50090.17940.6398-0.7421-0.914-0.34560.47270.50730.0654-0.0122-0.05320.26010.01540.2386-18.324411.342-10.3794
3814.7144.955910.321518.9473-2.93649.72320.1983-1.2997-0.07111.2665-0.3086-0.623-0.4895-0.90770.11030.3739-0.11810.01460.4240.06290.3025-23.72855.158-1.3623
3913.0597-4.9059-18.681.84387.025826.809-0.9537-1.0337-0.23680.33410.36860.11371.13151.45130.58520.64530.0033-0.59250.85050.09720.8149-21.795-2.2512.047
400.67080.51341.12295.6467-2.22073.78950.0779-0.2296-0.06790.0928-0.1573-0.09370.0864-0.24570.07950.1363-0.0407-0.01510.39870.10210.399-29.9683-2.1342-5.2964
413.88541.09984.11623.34211.499510.58920.1886-0.3237-0.1220.56280.02080.4257-0.1025-0.6243-0.20940.1597-0.01660.00840.4002-0.0750.2754-36.63587.0575-6.1623
426.8446-4.4593-0.24348.334-0.32624.79740.06420.1235-0.509-0.2912-0.1610.41030.3538-0.39770.09680.0531-0.0463-0.04780.1967-0.02270.2366-33.169-2.0378-15.3495
4334.674112.67871.450821.26030.98780.13490.687-0.3441-2.019-0.1019-0.6474-1.28490.27280.0377-0.03971.11780.2033-0.00150.280.10280.3656-25.449-8.2437-9.6838
448.4296-1.1426-5.01910.5631-3.00754.29950.2322-0.2663-0.25870.2295-0.6881-0.7966-0.20580.45030.45590.15470.0641-0.05570.33150.13630.3382-21.48720.5974-10.6008
4511.04936.1972-1.083628.3532-3.886720.32730.0090.7548-0.2805-0.9242-0.5796-0.69830.64140.46880.57070.08860.0689-0.02970.24950.06030.2834-21.51494.8391-17.9163
463.4382-1.38740.48524.00162.98343.0064-0.03680.0006-0.1041-0.2671-0.00950.0953-0.2634-0.03080.04640.1865-0.02710.01240.2010.01690.1304-12.090212.1845-32.5372
478.5325-4.6126-1.35257.07770.034516.7162-0.07520.40521.13-0.0123-0.3001-0.7203-1.80240.67490.37530.5117-0.1657-0.04020.33090.04540.3535-7.732922.4541-33.9234
487.64360.65832.98156.0297-1.29583.70410.27910.37080.1597-0.58160.0004-0.52920.30530.3197-0.27940.1555-0.02880.03710.2612-0.04250.2387-9.028831.1872-10.9518
4911.99061.68-1.518129.3719-0.542316.10780.0478-1.01630.2610.56830.14410.4749-0.286-0.566-0.19190.1332-0.096-0.02210.3304-0.00630.2425-19.275332.7565-6.943
503.36341.8594-0.95335.0631-3.30099.93140.1004-0.16630.01760.2334-0.06070.0802-0.1407-0.0656-0.03970.02060.0325-0.01690.163-0.02790.1715-29.176510.7657-11.6863
5117.547-6.79597.632716.35531.600217.31770.1171.663-0.2593-1.5018-0.1210.45060.2418-0.26650.0040.2819-0.017-0.04390.3912-0.03990.3103-31.3518.2814-22.318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 87
2X-RAY DIFFRACTION2A90 - 101
3X-RAY DIFFRACTION3A102 - 114
4X-RAY DIFFRACTION4A115 - 122
5X-RAY DIFFRACTION5A123 - 130
6X-RAY DIFFRACTION6A131 - 140
7X-RAY DIFFRACTION7A141 - 145
8X-RAY DIFFRACTION8A146 - 150
9X-RAY DIFFRACTION9A151 - 156
10X-RAY DIFFRACTION10A157 - 167
11X-RAY DIFFRACTION11A168 - 175
12X-RAY DIFFRACTION12A176 - 181
13X-RAY DIFFRACTION13A182 - 189
14X-RAY DIFFRACTION14A190 - 196
15X-RAY DIFFRACTION15A197 - 204
16X-RAY DIFFRACTION16B79 - 84
17X-RAY DIFFRACTION17B85 - 97
18X-RAY DIFFRACTION18B98 - 106
19X-RAY DIFFRACTION19B107 - 114
20X-RAY DIFFRACTION20B115 - 129
21X-RAY DIFFRACTION21B130 - 136
22X-RAY DIFFRACTION22B137 - 141
23X-RAY DIFFRACTION23B142 - 148
24X-RAY DIFFRACTION24B149 - 153
25X-RAY DIFFRACTION25B154 - 161
26X-RAY DIFFRACTION26B162 - 174
27X-RAY DIFFRACTION27B175 - 179
28X-RAY DIFFRACTION28B180 - 189
29X-RAY DIFFRACTION29B190 - 197
30X-RAY DIFFRACTION30B198 - 204
31X-RAY DIFFRACTION31C80 - 83
32X-RAY DIFFRACTION32C84 - 90
33X-RAY DIFFRACTION33C91 - 100
34X-RAY DIFFRACTION34C101 - 116
35X-RAY DIFFRACTION35C117 - 128
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