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- PDB-3m51: Structure of the 14-3-3/PMA2 complex stabilized by Pyrrolidone1 -

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Basic information

Entry
Database: PDB / ID: 3m51
TitleStructure of the 14-3-3/PMA2 complex stabilized by Pyrrolidone1
Components
  • 14-3-3-like protein C
  • N.plumbaginifolia H+-translocating ATPase mRNA
KeywordsPROTEIN BINDING / all helical / protein-protein complex
Function / homology
Function and homology information


P-type H+-exporting transporter / proton export across plasma membrane / P-type proton-exporting transporter activity / signal transduction / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
P-type ATPase, subfamily IIIA / 14-3-3 domain / Delta-Endotoxin; domain 1 / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / E1-E2 ATPase / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...P-type ATPase, subfamily IIIA / 14-3-3 domain / Delta-Endotoxin; domain 1 / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / E1-E2 ATPase / 14-3-3 proteins signature 2. / 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 / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-YR1 / 14-3-3-like protein C / Plasma membrane ATPase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
Nicotiana plumbaginifolia (curled-leaved tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 Å
AuthorsOttmann, C. / Rose, R. / Waldmann, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Identification and structure of small-molecule stabilizers of 14-3-3 protein-protein interactions
Authors: Rose, R. / Erdmann, S. / Bovens, S. / Wolf, A. / Rose, M. / Hennig, S. / Waldmann, H. / Ottmann, C.
History
DepositionMar 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3-like protein C
P: N.plumbaginifolia H+-translocating ATPase mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2273
Polymers30,7672
Non-polymers4601
Water1267
1
A: 14-3-3-like protein C
P: N.plumbaginifolia H+-translocating ATPase mRNA
hetero molecules

A: 14-3-3-like protein C
P: N.plumbaginifolia H+-translocating ATPase mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4546
Polymers61,5344
Non-polymers9212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Buried area6740 Å2
ΔGint-31 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.440, 97.440, 214.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein 14-3-3-like protein C / 14-3-3-like protein B


Mass: 27169.635 Da / Num. of mol.: 1 / Fragment: residues 1-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Plasmid: PPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P93343
#2: Protein/peptide N.plumbaginifolia H+-translocating ATPase mRNA


Mass: 3597.148 Da / Num. of mol.: 1 / Fragment: C-terminal fragment / Mutation: S938A,T955D,V956I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana plumbaginifolia (curled-leaved tobacco)
Plasmid: PTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q42932
#3: Chemical ChemComp-YR1 / 2-hydroxy-5-[(5S)-3-hydroxy-5-(4-nitrophenyl)-2-oxo-4-(phenylcarbonyl)-2,5-dihydro-1H-pyrrol-1-yl]benzoic acid


Mass: 460.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H16N2O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 4.13 Å3/Da / Density % sol: 70.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M CHES, 1.0M Na-Citrat, 30%(w/v) sucrose, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00749 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00749 Å / Relative weight: 1
ReflectionResolution: 3.25→48.74 Å / Num. obs: 8499 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 85.969 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 22.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.25-3.50.474.613333163699.9
3.5-40.18811.1179752206100
4-50.07524.7177152206100
5-100.03538.7163622111100
10-150.02266.91610228100
15-200.02563.441063100
200.02556.82814990.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YZ5

1yz5


Resolution: 3.25→48.74 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.324 / WRfactor Rwork: 0.295 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.737 / SU Rfree: 0.567 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.567 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.34 425 5 %RANDOM
Rwork0.31 ---
obs0.312 8496 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 116.37 Å2 / Biso mean: 98.388 Å2 / Biso min: 54.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2---0.65 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 3.25→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 34 7 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0222074
X-RAY DIFFRACTIONr_angle_refined_deg0.6461.9922795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4855247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59924.54599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54815389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0661515
X-RAY DIFFRACTIONr_chiral_restr0.0430.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021542
X-RAY DIFFRACTIONr_mcbond_it0.2441.51247
X-RAY DIFFRACTIONr_mcangle_it0.4421998
X-RAY DIFFRACTIONr_scbond_it0.1783827
X-RAY DIFFRACTIONr_scangle_it0.3254.5797
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 30 -
Rwork0.403 567 -
all-597 -
obs--100 %

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