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- PDB-2o8p: Crystal structure of a putative 14-3-3 protein from Cryptosporidi... -

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Basic information

Entry
Database: PDB / ID: 2o8p
TitleCrystal structure of a putative 14-3-3 protein from Cryptosporidium parvum, cgd7_2470
Components14-3-3 domain containing protein
KeywordsSIGNALING PROTEIN / 14-3-3 / cell regulator protein / Cryptosporidium parvum / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha / 14-3-3 domain containing protein
Function and homology information
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsDong, A. / Lew, J. / Wasney, G. / Lin, L. / Hassanali, A. / Zhao, Y. / Vedadi, M. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. ...Dong, A. / Lew, J. / Wasney, G. / Lin, L. / Hassanali, A. / Zhao, Y. / Vedadi, M. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Walker, J.R. / Bochkarev, A. / Hui, R. / Brokx, S.J. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2011
Title: Characterization of 14-3-3 proteins from Cryptosporidium parvum.
Authors: Brokx, S.J. / Wernimont, A.K. / Dong, A. / Wasney, G.A. / Lin, Y.H. / Lew, J. / Vedadi, M. / Lee, W.H. / Hui, R.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 domain containing protein


Theoretical massNumber of molelcules
Total (without water)27,2001
Polymers27,2001
Non-polymers00
Water4,234235
1
A: 14-3-3 domain containing protein

A: 14-3-3 domain containing protein


Theoretical massNumber of molelcules
Total (without water)54,3992
Polymers54,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
Unit cell
Length a, b, c (Å)87.325, 87.325, 167.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

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Components

#1: Protein 14-3-3 domain containing protein


Mass: 27199.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Plasmid: p15-tev-lic DERIVED FROM PET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta-R3 / References: UniProt: Q5CYG0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 3350, 0.3 M ammonium acetate, 0.2 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2006
RadiationMonochromator: Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 28702 / Num. obs: 28702 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 9
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2507 / Rsym value: 0.859 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
Coot0.1.2model building
RefinementMethod to determine structure: SAD / Resolution: 1.82→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.513 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23911 757 2.6 %RANDOM
Rwork0.19781 ---
all0.19894 27920 --
obs0.19894 27920 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 0 235 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221884
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9692533
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0415230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.33525.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7315374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.824158
X-RAY DIFFRACTIONr_chiral_restr0.080.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021402
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2939
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21351
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2151.51182
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61221825
X-RAY DIFFRACTIONr_scbond_it3.0493806
X-RAY DIFFRACTIONr_scangle_it4.6414.5708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.823→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 45 -
Rwork0.247 1775 -
obs--86.17 %

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