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- PDB-2w1z: ROP2 from Toxoplasma gondii: A virulence factor with a protein- k... -

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Basic information

Entry
Database: PDB / ID: 2w1z
TitleROP2 from Toxoplasma gondii: A virulence factor with a protein- kinase fold and no enzymatic activity.
ComponentsROP2
KeywordsTRANSFERASE / INACTIVITY / PROTEIN-KINASE / MEMBRANE-ATTACHMENT
Function / homology
Function and homology information


protein kinase activity / ATP binding
Similarity search - Function
Rhoptry protein, Rop2-like / Protein kinase-like domain, Apicomplexa / Kinase-like / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily ...Rhoptry protein, Rop2-like / Protein kinase-like domain, Apicomplexa / Kinase-like / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.97 Å
AuthorsLabesse, G. / Gelin, M. / Bessin, Y. / Lebrun, M. / Arold, S.T. / Dubremetz, J.-F.
CitationJournal: Structure / Year: 2009
Title: Rop2 from Toxoplasma Gondii: A Virulence Factor with a Protein-Kinase Fold and No Enzymatic Activity.
Authors: Labesse, G. / Gelin, M. / Bessin, Y. / Lebrun, M. / Papoin, J. / Cerdan, R. / Arold, S.T. / Dubremetz, J.-F.
History
DepositionOct 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 21, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Refinement description / Structure summary
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ROP2
B: ROP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6206
Polymers85,2352
Non-polymers3844
Water9,440524
1
A: ROP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7142
Polymers42,6181
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ROP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9064
Polymers42,6181
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)187.609, 51.348, 125.582
Angle α, β, γ (deg.)90.00, 128.65, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A194 - 364
2116B194 - 364

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Components

#1: Protein ROP2


Mass: 42617.648 Da / Num. of mol.: 2 / Fragment: PROTEIN-KINASE DOMAIN, RESIDUES 195-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Description: STRAIN RH / Plasmid: PQE31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q27007, Transferases; Transferring phosphorus-containing groups
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.96 Å3/Da / Density % sol: 58.4 % / Description: NONE
Crystal growpH: 5.6
Details: 320 MM AMMONIUM CITRATE, PH 5.6, 2% MPD, 15% W/V POLYETHYLENE GLYCOL 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976255
DetectorType: ADSC CCD / Detector: CCD / Date: May 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976255 Å / Relative weight: 1
ReflectionResolution: 1.97→73.32 Å / Num. obs: 66543 / % possible obs: 82.7 % / Observed criterion σ(I): 1.1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.1
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.5 / % possible all: 65.9

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Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.97→73.32 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.577 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 2766 5.1 %RANDOM
Rwork0.19339 ---
obs0.19577 51992 82.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.154 Å2
Baniso -1Baniso -2Baniso -3
1--2.94 Å20 Å2-1.85 Å2
2--0.73 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.97→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5809 0 20 524 6353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226042
X-RAY DIFFRACTIONr_bond_other_d0.0080.024237
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9658198
X-RAY DIFFRACTIONr_angle_other_deg1.9853.00110217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38522.389314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.645151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2641576
X-RAY DIFFRACTIONr_chiral_restr0.1590.2897
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021309
X-RAY DIFFRACTIONr_nbd_refined0.1880.21257
X-RAY DIFFRACTIONr_nbd_other0.2010.24403
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22814
X-RAY DIFFRACTIONr_nbtor_other0.0910.23040
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2374
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.491.53561
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86125786
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.14332481
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7444.52412
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2412 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.615
2Bloose positional0.615
1Aloose thermal1.4310
2Bloose thermal1.4310
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 150
Rwork0.319 2806
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)
11.5736-0.53370.05243.3944-1.37762.5354-0.08580.35930.0534-0.14980.16410.10190.0356-0.3586-0.07830.03240.00610.063-0.00820.0047-0.2398-16.97440.48432.877
21.9282-0.2386-0.63911.27740.36421.54840.043-0.0727-0.0647-0.0553-0.0111-0.041-0.0414-0.0696-0.03190.0937-0.01540.1336-0.1910.0093-0.1753-3.18730.2253.722
32.01140.810.20943.28490.37091.46150.0737-0.42120.09730.1884-0.1136-0.1637-0.06610.16190.0399-0.0073-0.05030.0896-0.0370.0138-0.2537-20.76713.21313.102
41.42650.393-0.66621.321-0.37851.36820.05810.0381-0.0229-0.0038-0.01890.0336-0.03580.048-0.03920.08520.01210.1341-0.18790.0108-0.1738-36.4492.742-6.036
50.20070.07680.16810.20170.15190.1854-0.0025-0.01230.0064-0.0174-0.0164-0.0019-0.0203-0.02070.01890.2533-0.01890.1742-0.01330.0218-0.0139-20.33217.16821.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A223 - 360
2X-RAY DIFFRACTION2A196 - 220
3X-RAY DIFFRACTION2A361 - 556
4X-RAY DIFFRACTION3B223 - 360
5X-RAY DIFFRACTION4B196 - 220
6X-RAY DIFFRACTION4B361 - 557
7X-RAY DIFFRACTION5A - B2001 - 2296

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