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- PDB-5by9: The crystal structure of polyglycilated 14-3-3 protein from Giard... -

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Basic information

Entry
Database: PDB / ID: 5by9
TitleThe crystal structure of polyglycilated 14-3-3 protein from Giardia intestinalis
Components14-3-3 protein
KeywordsSIGNALING PROTEIN / HOMODIMER / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


signal transduction / cytoplasm
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative 14-3-3 domain protein
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4 Å
AuthorsFiorillo, A. / Ilari, A. / Lalle, M.
CitationJournal: J.Chem.Inf.Model. / Year: 2015
Title: Molecular Dynamics Simulations and Structural Analysis of Giardia duodenalis 14-3-3 Protein-Protein Interactions.
Authors: Cau, Y. / Fiorillo, A. / Mori, M. / Ilari, A. / Botta, M. / Lalle, M.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein
B: 14-3-3 protein
C: 14-3-3 protein
D: 14-3-3 protein


Theoretical massNumber of molelcules
Total (without water)115,6984
Polymers115,6984
Non-polymers00
Water00
1
A: 14-3-3 protein
B: 14-3-3 protein


Theoretical massNumber of molelcules
Total (without water)57,8492
Polymers57,8492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: 14-3-3 protein
D: 14-3-3 protein


Theoretical massNumber of molelcules
Total (without water)57,8492
Polymers57,8492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.207, 100.207, 140.955
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA13 - 3313 - 33
21METMETILEILEBB13 - 3313 - 33
31METMETILEILECC13 - 3313 - 33
41METMETILEILEDD13 - 3313 - 33
12LYSLYSTRPTRPAA43 - 6343 - 63
22LYSLYSTRPTRPBB43 - 6343 - 63
32LYSLYSTRPTRPCC43 - 6343 - 63
42LYSLYSTRPTRPDD43 - 6343 - 63
13GLUGLULEULEUAA85 - 21085 - 210
23GLUGLULEULEUBB85 - 21085 - 210
33GLUGLULEULEUCC85 - 21085 - 210
43GLUGLULEULEUDD85 - 21085 - 210

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.494334, 0.851943, 0.172704), (0.847898, -0.516353, 0.120202), (0.191581, 0.087015, -0.977612)36.264721, -61.835339, -3.06385
3given(-0.534868, -0.843262, -0.053162), (-0.839269, 0.537503, -0.081963), (0.097691, 0.000778, -0.995217)46.19001, -30.62031, -2.10379
4given(-0.97568, 0.05961, -0.210938), (-0.041831, -0.995262, -0.087771), (-0.215171, -0.076813, 0.973551)31.357201, -6.37805, 1.89492

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Components

#1: Protein
14-3-3 protein / Putative 14-3-3 domain protein


Mass: 28924.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Gene: DHA2_6430, GSB_6430 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2QBT8

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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: 3.74 Å3/Da / Density % sol: 67.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: LiCl 1M, hepes pH 7, PEG6K 10%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.571
11K, H, -L20.429
ReflectionResolution: 4→40 Å / Num. obs: 12386 / % possible obs: 92.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.154 / Χ2: 1.252 / Net I/av σ(I): 5.133 / Net I/σ(I): 5.3 / Num. measured all: 23764
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
4-4.141.90.40611301.21384.4
4.14-4.311.90.43812151.27991.8
4.31-4.51.90.33212121.51291
4.5-4.741.90.29312741.40394.5
4.74-5.041.90.22612651.2994.7
5.04-5.431.90.26212791.31294.3
5.43-5.971.90.28812681.19795.4
5.97-6.8320.16912501.18593.8
6.83-8.591.90.06612850.89595.2
8.59-401.90.03512081.25590.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 4→36.95 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.905 / SU B: 28.235 / SU ML: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 613 5 %RANDOM
Rwork0.2325 ---
obs0.2326 11755 92.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120 Å2 / Biso mean: 117.648 Å2 / Biso min: 99.09 Å2
Baniso -1Baniso -2Baniso -3
1-46.99 Å20 Å20 Å2
2--46.99 Å20 Å2
3----93.98 Å2
Refinement stepCycle: final / Resolution: 4→36.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7633 0 0 0 7633
Num. residues----937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197763
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.97210453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1175933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.31424.169403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44151459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0091568
X-RAY DIFFRACTIONr_chiral_restr0.060.21126
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215894
X-RAY DIFFRACTIONr_mcbond_it0.52511.7623744
X-RAY DIFFRACTIONr_mcangle_it0.92617.6424673
X-RAY DIFFRACTIONr_scbond_it0.411.7714019
Refine LS restraints NCS

Ens-ID: 1 / Number: 1370 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.30.5
2BMEDIUM POSITIONAL0.320.5
3CMEDIUM POSITIONAL0.350.5
4DMEDIUM POSITIONAL0.350.5
1AMEDIUM THERMAL3.172
2BMEDIUM THERMAL2.042
3CMEDIUM THERMAL2.472
4DMEDIUM THERMAL2.042
LS refinement shellResolution: 4→4.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 38 -
Rwork0.267 774 -
all-812 -
obs--84.41 %

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