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Basic information

Entry
Database: PDB / ID: 3hgf
TitleExpression, purification, spectroscopical and crystallographical studies of segments of the nucleotide binding domain of the reticulocyte binding protein Py235 of Plasmodium yoelii
ComponentsRhoptry protein fragment
KeywordsNUCLEOTIDE BINDING PROTEIN / helix-turn-helix
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #560 / Reticulocyte binding protein / Rh5 coiled-coil domain / Rh5 coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / membrane / Rhoptry protein
Function and homology information
Biological speciesPlasmodium yoelii yoelii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4 Å
AuthorsGruber, A. / Manimekalai, M.S.S. / Balakrishna, A.M. / Hunke, C. / Jeyakanthan, J. / Preiser, P.R. / Gruber, G.
Citation
Journal: Plos One / Year: 2010
Title: Structural determination of functional units of the nucleotide binding domain (NBD94) of the reticulocyte binding protein Py235 of Plasmodium yoelii
Authors: Gruber, A. / Manimekalai, M.S.S. / Balakrishna, A.M. / Hunke, C. / Jeyakanthan, J. / Preiser, P.R. / Gruber, G.
#1: Journal: J.Biol.Chem. / Year: 2008
Title: ATP/ADP binding to a novel nucleotide binding domain of the reticulocyte-binding protein Py235 of Plasmodium yoelii
Authors: Ramalingam, J.K. / Hunke, C. / Gao, X. / Gruber, G. / Preiser, P.R.
History
DepositionMay 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhoptry protein fragment
B: Rhoptry protein fragment
C: Rhoptry protein fragment


Theoretical massNumber of molelcules
Total (without water)38,6073
Polymers38,6073
Non-polymers00
Water00
1
A: Rhoptry protein fragment


Theoretical massNumber of molelcules
Total (without water)12,8691
Polymers12,8691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rhoptry protein fragment


Theoretical massNumber of molelcules
Total (without water)12,8691
Polymers12,8691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Rhoptry protein fragment


Theoretical massNumber of molelcules
Total (without water)12,8691
Polymers12,8691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.223, 70.223, 193.218
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Rhoptry protein fragment / Retyculocyte-binding protein homologue Py235


Mass: 12868.979 Da / Num. of mol.: 3 / Fragment: Nucleotide-binding domain, UNP residues 1168-1265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii yoelii (eukaryote) / Strain: Plasmodium yoelii yoelii strain YM / Gene: Plasmodium yoelii gene / Plasmid: pET9d1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7RPU0

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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: 1.7811 Å3/Da / Density % sol: 30.9413 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 35% (v/v) 2-methyl-2,4-pentanediol, 0.1M acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.97898 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 2825 / % possible obs: 95.6 % / Redundancy: 15.4 % / Biso Wilson estimate: 81.82 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 13.712
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.69 / % possible all: 97.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 4→33 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.864 / Occupancy max: 1 / Occupancy min: 1 / SU B: 131.155 / SU ML: 1.882 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R Free: 1.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. 2. Assigned only the Back bone atoms for all the residues since the side chains are not visible in the electron density map.
RfactorNum. reflection% reflectionSelection details
Rfree0.37324 127 4.9 %RANDOM
Rwork0.33906 ---
obs0.34864 2482 95.39 %-
all-2738 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 4→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 0 0 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021372
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8391.9431910
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5365267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0470.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021080
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.001→4.214 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.443 16 -
Rwork0.39 336 -
obs--93.87 %

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