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- PDB-4dx0: Structure of the 14-3-3/PMA2 complex stabilized by a pyrazole der... -

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Basic information

Entry
Database: PDB / ID: 4dx0
TitleStructure of the 14-3-3/PMA2 complex stabilized by a pyrazole derivative
Components
  • 14-3-3-like protein E
  • N.plumbaginifolia H+-translocating ATPase mRNA
KeywordsPROTEIN BINDING/Hydrolase / 14-3-3 fold / Pyrrolidinones / PROTEIN BINDING-Hydrolase complex
Function / homology
Function and homology information


P-type H+-exporting transporter / proton export across plasma membrane / P-type proton-exporting transporter activity / regulation of intracellular pH / ATP hydrolysis activity / ATP binding / plasma membrane
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-0MT / 14-3-3-like protein E / Plasma membrane ATPase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
Nicotiana plumbaginifolia (curled-leaved tobacco)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsRichter, A. / Rose, R. / Hedberg, C. / Waldmann, H. / Ottmann, C.
CitationJournal: Chemistry / Year: 2012
Title: An Optimised Small-Molecule Stabiliser of the 14-3-3-PMA2 Protein-Protein Interaction.
Authors: Richter, A. / Rose, R. / Hedberg, C. / Waldmann, H. / Ottmann, C.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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 / pdbx_initial_refinement_model / 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 1.2Dec 13, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,5233
Polymers31,0822
Non-polymers4401
Water00
1
A: 14-3-3-like protein E
P: N.plumbaginifolia H+-translocating ATPase mRNA
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)63,0456
Polymers62,1644
Non-polymers8812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Buried area6990 Å2
ΔGint-34 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.450, 98.450, 216.710
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 E


Mass: 27485.025 Da / Num. of mol.: 1 / Fragment: UNP residues 1-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: O49997
#2: Protein/peptide N.plumbaginifolia H+-translocating ATPase mRNA


Mass: 3597.148 Da / Num. of mol.: 1 / Fragment: UNP residues 926-956 / Mutation: T955D, V956I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana plumbaginifolia (curled-leaved tobacco)
Production host: Escherichia coli (E. coli) / References: UniProt: Q42932, EC: 3.6.3.6
#3: Chemical ChemComp-0MT / 4-[(4R)-4-(4-nitrophenyl)-6-oxidanylidene-3-phenyl-1,4-dihydropyrrolo[3,4-c]pyrazol-5-yl]benzoic acid


Mass: 440.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H16N4O5

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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: 4.22 Å3/Da / Density % sol: 70.88 %
Crystal growTemperature: 277 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 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Feb 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. all: 7687 / Num. obs: 7386 / % possible obs: 96.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 102.446 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.98
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.4-3.60.4453.7772841131197.6
3.6-3.80.3175.475973935197.3
3.8-40.2088.124692733196.6
4-50.11614.03134922175195.1
5-100.04822.67125812120197.8
10-150.03432.551267229198.3
15-200.03130.5331763196.9

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Phasing

PhasingMethod: molecular replacement
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 7386
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.47-10037.70.86501
6.73-8.47490.753501
5.87-6.7358.50.68503
5.33-5.8756.50.638507
4.93-5.3357.90.654501
4.63-4.9359.40.606506
4.39-4.6370.10.566512
4.19-4.3969.40.554506
4.01-4.1970.40.532508
3.87-4.0174.60.438502
3.75-3.8771.10.429509
3.64-3.7568.80.551517
3.54-3.6462.10.64506
3.4-3.5467.20.626807

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
DM6.1phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3M51

3m51


Resolution: 3.4→19.83 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.843 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 71.259 / SU ML: 1.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.758 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3992 370 5 %RANDOM
Rwork0.3556 ---
all0.3577 7687 --
obs0.3577 7386 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: 177.59 Å2 / Biso mean: 143.2814 Å2 / Biso min: 117.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 33 0 2103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222144
X-RAY DIFFRACTIONr_angle_refined_deg0.8971.992895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0665259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46124.804102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87315398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2951514
X-RAY DIFFRACTIONr_chiral_restr0.0560.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021605
X-RAY DIFFRACTIONr_mcbond_it2.2461.51298
X-RAY DIFFRACTIONr_mcangle_it2.98222081
X-RAY DIFFRACTIONr_scbond_it0.1083846
X-RAY DIFFRACTIONr_scangle_it0.1974.5814
LS refinement shellResolution: 3.4→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 26 -
Rwork0.499 495 -
all-521 -
obs--100 %

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