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- PDB-4f7r: Crystal structure of 14-3-3 protein from Giardia intestinalis -

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Basic information

Entry
Database: PDB / ID: 4f7r
TitleCrystal structure of 14-3-3 protein from Giardia intestinalis
Components14-3-3 protein
KeywordsSIGNALING PROTEIN / 9-alpha-helix / 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 / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFiorillo, A. / Ilari, A. / Lalle, M.
CitationJournal: 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 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Apr 1, 2015Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,63220
Polymers116,0954
Non-polymers1,53716
Water00
1
A: 14-3-3 protein
B: 14-3-3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,91211
Polymers58,0472
Non-polymers8659
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-120 kcal/mol
Surface area26570 Å2
MethodPISA
2
C: 14-3-3 protein
D: 14-3-3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7209
Polymers58,0472
Non-polymers6727
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-91 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.879, 100.879, 140.559
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRGLYGLY3AA10 - 3515 - 40
211TYRTYRGLYGLY3BB10 - 3515 - 40
311TYRTYRGLYGLY3CC10 - 3515 - 40
121LEULEUGLUGLU3AA40 - 7045 - 75
221LEULEUGLUGLU3BB40 - 7045 - 75
321LEULEUGLUGLU3CC40 - 7045 - 75
131GLNGLNTYRTYR3AA86 - 14091 - 145
231GLNGLNTYRTYR3BB86 - 14091 - 145
331GLNGLNTYRTYR3CC86 - 14091 - 145
141GLUGLUTHRTHR3AA147 - 208152 - 213
241GLUGLUTHRTHR3BB147 - 208152 - 213
341GLUGLUTHRTHR3CC147 - 208152 - 213
151SERSERASNASN5AA221 - 233226 - 238
251SERSERASNASN5BB221 - 233226 - 238
351SERSERASNASN5CC221 - 233226 - 238
112TYRTYRGLYGLY5AA10 - 3515 - 40
212TYRTYRGLYGLY5DD10 - 3515 - 40
122LEULEUGLUGLU4AA40 - 7045 - 75
222LEULEUGLUGLU4DD40 - 7045 - 75
132GLNGLNTYRTYR4AA86 - 14091 - 145
232GLNGLNTYRTYR4DD86 - 14091 - 145
142LYSLYSALAALA4AA148 - 206153 - 211
242LYSLYSALAALA4DD148 - 206153 - 211
152SERSERASNASN5AA221 - 233226 - 238
252SERSERASNASN5DD221 - 233226 - 238

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.482498, -0.858673, 0.172847), (-0.857851, -0.503115, -0.10472), (0.176883, -0.09775, -0.979366)14.1366, 24.42003, -3.25733
3given(-0.536446, 0.842018, -0.056853), (0.836399, 0.53943, 0.097216), (0.112526, 0.004599, -0.993638)6.41969, -60.24574, -3.67889

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Components

#1: Protein
14-3-3 protein


Mass: 29023.725 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q2QBT8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2007
RadiationMonochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 26426 / Num. obs: 26426 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 87.1 Å2 / Rsym value: 0.125 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.2-3.316.92.80.7621100
3.31-3.4574.30.5071100
3.45-3.676.20.3571100
3.6-3.7978.50.2551100
3.79-4.03712.90.1611100
4.03-4.34717.90.1071100
4.34-4.78720.50.0911100
4.78-5.477210.091100
5.47-6.89721.90.0851100
6.89-50753.70.0331100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 18.364 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1338 5.1 %RANDOM
Rwork0.185 ---
obs0.18741 25056 99.96 %-
all-25056 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.463 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å21.18 Å20 Å2
2--2.36 Å20 Å2
3----3.54 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7716 0 80 0 7796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.027918
X-RAY DIFFRACTIONr_bond_other_d0.0010.025515
X-RAY DIFFRACTIONr_angle_refined_deg0.7991.9810676
X-RAY DIFFRACTIONr_angle_other_deg0.752313375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4455946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53524.201407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.563151473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9971568
X-RAY DIFFRACTIONr_chiral_restr0.0440.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021629
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A78MEDIUM POSITIONAL0.720.5
12B78MEDIUM POSITIONAL0.680.5
13C78MEDIUM POSITIONAL0.340.5
11A1494LOOSE POSITIONAL0.465
12B1494LOOSE POSITIONAL0.495
13C1494LOOSE POSITIONAL0.445
11A1033TIGHT THERMAL3.390.5
12B1033TIGHT THERMAL4.590.5
13C1033TIGHT THERMAL2.920.5
11A78MEDIUM THERMAL3.182
12B78MEDIUM THERMAL1.42
13C78MEDIUM THERMAL3.222
11A1494LOOSE THERMAL3.8210
12B1494LOOSE THERMAL4.9210
13C1494LOOSE THERMAL3.310
21A2259MEDIUM POSITIONAL0.40.5
21A308LOOSE POSITIONAL0.555
21A2259MEDIUM THERMAL8.632
21A308LOOSE THERMAL5.7910
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 91 -
Rwork0.292 1880 -
obs--99.8 %

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