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- PDB-4zq0: crystal structure of Giardia 14-3-3 in complex with the phosphope... -

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Basic information

Entry
Database: PDB / ID: 4zq0
Titlecrystal structure of Giardia 14-3-3 in complex with the phosphopeptide A8Ap
Components
  • 14-3-3 protein
  • A8Ap phosphopeptide
KeywordsSIGNALING PROTEIN / phosphopeptide binding protein-protein interaction
Function / homology
Function and homology information


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
PHOSPHATE ION / 14-3-3 protein / Putative 14-3-3 domain protein
Similarity search - Component
Biological speciesGiardia lamblia P15 (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsFiorillo, A. / Ilari, A.
Citation
Journal: 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.
#1: Journal: Plos One / Year: 2014
Title: The crystal structure of Giardia duodenalis 14-3-3 in the apo form: when protein post-translational modifications make the difference.
Authors: Fiorillo, A. / di Marino, D. / Bertuccini, L. / Via, A. / Pozio, E. / Camerini, S. / Ilari, A. / Lalle, M.
History
DepositionMay 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein
C: 14-3-3 protein
B: 14-3-3 protein
D: 14-3-3 protein
E: A8Ap phosphopeptide
F: A8Ap phosphopeptide
G: A8Ap phosphopeptide
H: A8Ap phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0419
Polymers111,9468
Non-polymers951
Water00
1
A: 14-3-3 protein
B: 14-3-3 protein
E: A8Ap phosphopeptide
F: A8Ap phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0685
Polymers55,9734
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: 14-3-3 protein
D: 14-3-3 protein
G: A8Ap phosphopeptide
H: A8Ap phosphopeptide


Theoretical massNumber of molelcules
Total (without water)55,9734
Polymers55,9734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.958, 109.408, 78.568
Angle α, β, γ (deg.)90.000, 92.640, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31B
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
11TYRTYRLYSLYSAA10 - 726 - 68
21TYRTYRLYSLYSCB10 - 726 - 68
31TYRTYRLYSLYSBC10 - 726 - 68
41TYRTYRLYSLYSDD10 - 726 - 68
12GLUGLUGLUGLUAA85 - 13981 - 135
22GLUGLUGLUGLUCB85 - 13981 - 135
32GLUGLUGLUGLUBC85 - 13981 - 135
42GLUGLUGLUGLUDD85 - 13981 - 135
13ILEILETHRTHRAA149 - 208145 - 204
23ILEILETHRTHRCB149 - 208145 - 204
33ILEILETHRTHRBC149 - 208145 - 204
43ILEILETHRTHRDD149 - 208145 - 204
14ASPASPLEULEUAA220 - 234216 - 230
24ASPASPLEULEUCB220 - 234216 - 230
34ASPASPLEULEUBC220 - 234216 - 230
44ASPASPLEULEUDD220 - 234216 - 230

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.887526, 0.202928, -0.413664), (0.00891, -0.890064, -0.455748), (-0.460671, -0.408174, 0.788147)74.551804, -5.26268, 45.91032
3given(0.711351, 0.498669, 0.495287), (0.494298, -0.855928, 0.151842), (0.499649, 0.136806, -0.855357)1.51842, -13.65746, 8.44367
4given(-0.849976, -0.524428, -0.050154), (-0.509761, 0.794686, 0.329573), (-0.132981, 0.305695, -0.942797)75.156532, 34.252701, 11.32848

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Components

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


Mass: 27191.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: a stretch of 10 glycines was added at the C-ter / Source: (gene. exp.) Giardia lamblia P15 (eukaryote) / Gene: DHA2_6430, GSB_6430 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2QBT8, UniProt: E1F4V5*PLUS
#2: Protein/peptide
A8Ap phosphopeptide


Mass: 794.770 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG 5000 MME 25% w/v, Lithium acetate 0.2 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 3.1→48.01 Å / Num. obs: 21585 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.069 / Net I/σ(I): 10.3 / Num. measured all: 113267
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.1-3.315.30.91322082439020.7120.437100
8.77-48.014.80.03434.747239800.9990.01899.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimless0.3.8data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7R

4f7r


Resolution: 3.1→48.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.514 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 1093 5.1 %RANDOM
Rwork0.2033 ---
obs0.2066 20475 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110 Å2 / Biso mean: 79.773 Å2 / Biso min: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å20.77 Å2
2--2.9 Å20 Å2
3----1.62 Å2
Refinement stepCycle: final / Resolution: 3.1→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7703 0 5 0 7708
Biso mean--54.87 --
Num. residues----947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197836
X-RAY DIFFRACTIONr_bond_other_d00.027494
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.97910564
X-RAY DIFFRACTIONr_angle_other_deg3.597317242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5524.16399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.146151455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6551568
X-RAY DIFFRACTIONr_chiral_restr0.0630.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028828
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021788
X-RAY DIFFRACTIONr_mcbond_it3.0027.8183780
X-RAY DIFFRACTIONr_mcbond_other3.0027.8183779
X-RAY DIFFRACTIONr_mcangle_it4.84511.7354711
Refine LS restraints NCS

Ens-ID: 1 / Number: 3097 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.540.5
2CMEDIUM POSITIONAL0.520.5
3BMEDIUM POSITIONAL0.520.5
4DMEDIUM POSITIONAL0.530.5
1AMEDIUM THERMAL9.992
2CMEDIUM THERMAL6.352
3BMEDIUM THERMAL7.432
4DMEDIUM THERMAL13.872
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 59 -
Rwork0.327 1546 -
all-1605 -
obs--100 %

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