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- PDB-4chj: Structure of Inner Membrane Complex (IMC) Sub-compartment Protein... -

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Basic information

Entry
Database: PDB / ID: 4chj
TitleStructure of Inner Membrane Complex (IMC) Sub-compartment Protein 3 (ISP3) from Toxoplasma gondii
ComponentsIMC SUB-COMPARTMENT PROTEIN ISP3
KeywordsCELL CYCLE / PARASITE / CELL DIVISION / ENDODYOGENY / PLECKSTRIN HOMOLOGY (PH) FOLD
Function / homologyISP3, C-terminal / ISP3 C-terminal / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta / IMC sub-compartment protein ISP3 / IMC sub-compartment protein ISP3
Function and homology information
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsTonkin, M.L. / Beck, J.R. / Bradley, P.J. / Boulanger, M.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Inner Membrane Complex Sub-Compartment Proteins Critical for Replication of the Apicomplexan Parasite Toxoplasma Gondii Adopt a Pleckstrin Homology Fold
Authors: Tonkin, M.L. / Beck, J.R. / Bradley, P.J. / Boulanger, M.J.
History
DepositionDec 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMC SUB-COMPARTMENT PROTEIN ISP3


Theoretical massNumber of molelcules
Total (without water)18,3291
Polymers18,3291
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.480, 99.480, 60.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein IMC SUB-COMPARTMENT PROTEIN ISP3 / TGISP3


Mass: 18329.406 Da / Num. of mol.: 1 / Fragment: PH DOMAIN, RESIDUES 10-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: ME49 / Plasmid: MODIFIED PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: S8EX33, UniProt: B9PJE6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.75 % / Description: NONE
Crystal growpH: 7
Details: 2.0 M SODIUM MALONATE PH 7.0, 10 MM BETAINE HYDROCHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.32→35.94 Å / Num. obs: 6813 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.6
Reflection shellResolution: 2.32→2.41 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.3 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TGISP1

Resolution: 2.32→35.94 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.278 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26797 324 4.8 %RANDOM
Rwork0.21817 ---
obs0.22052 6481 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.489 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.32→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 0 4 998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191009
X-RAY DIFFRACTIONr_bond_other_d0.0040.02966
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9571353
X-RAY DIFFRACTIONr_angle_other_deg0.61232217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3185121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46924.6354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.72315183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.177158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 22 -
Rwork0.302 454 -
obs--97.34 %

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