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- PDB-6ens: Structure of mouse wild-type RKIP -

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Basic information

Entry
Database: PDB / ID: 6ens
TitleStructure of mouse wild-type RKIP
ComponentsPhosphatidylethanolamine-binding protein 1
KeywordsSIGNALING PROTEIN / RKIP / PEBP / PBP
Function / homology
Function and homology information


positive regulation of acetylcholine metabolic process / positive regulation of acetylcholine biosynthetic process / positive regulation of cAMP-mediated signaling / Negative regulation of MAPK pathway / MAP2K and MAPK activation / regulation of the force of heart contraction / receptor serine/threonine kinase binding / mitogen-activated protein kinase binding / sperm capacitation / negative regulation of protein phosphorylation ...positive regulation of acetylcholine metabolic process / positive regulation of acetylcholine biosynthetic process / positive regulation of cAMP-mediated signaling / Negative regulation of MAPK pathway / MAP2K and MAPK activation / regulation of the force of heart contraction / receptor serine/threonine kinase binding / mitogen-activated protein kinase binding / sperm capacitation / negative regulation of protein phosphorylation / negative regulation of MAPK cascade / axon terminus / positive regulation of mitotic nuclear division / serine-type endopeptidase inhibitor activity / kinase binding / apical part of cell / MAPK cascade / synaptic vesicle / myelin sheath / mitochondrial outer membrane / signaling receptor binding / neuronal cell body / lipid binding / protein kinase binding / cell surface / extracellular space / ATP binding
Similarity search - Function
Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein family signature. / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Phosphatidylethanolamine-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHirschbeck, M. / Koelmel, W. / Schindelin, H. / Lorenz, K. / Kisker, C.
Funding support United States, Germany, 3items
OrganizationGrant numberCountry
National Institutes of HealthGM087630 United States
National Institutes of HealthGM55694 United States
German Research FoundationFZ82 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome.
Authors: Skinner, J.J. / Wang, S. / Lee, J. / Ong, C. / Sommese, R. / Sivaramakrishnan, S. / Koelmel, W. / Hirschbeck, M. / Schindelin, H. / Kisker, C. / Lorenz, K. / Sosnick, T.R. / Rosner, M.R.
History
DepositionOct 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylethanolamine-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9264
Polymers21,6821
Non-polymers2433
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-2 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.580, 54.090, 97.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylethanolamine-binding protein 1 / PEBP-1 / HCNPpp / Raf Kinase Inhibitory Protein


Mass: 21682.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pebp1, Pbp, Pebp / Production host: Escherichia coli (E. coli) / References: UniProt: P70296
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 6000, sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.3→23.06 Å / Num. obs: 42630 / % possible obs: 98.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.6
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IQY

2iqy


Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.945 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16809 2148 5.1 %RANDOM
Rwork0.12478 ---
obs0.12695 40315 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0 Å2
2---0.55 Å20 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 16 250 1717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191704
X-RAY DIFFRACTIONr_bond_other_d0.0020.021625
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9782350
X-RAY DIFFRACTIONr_angle_other_deg0.9953.0023749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81725.38578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20515286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.771157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212008
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02367
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_it1.071.272836
X-RAY DIFFRACTIONr_mcbond_other1.0934.768834
X-RAY DIFFRACTIONr_mcangle_it1.3991.9121065
X-RAY DIFFRACTIONr_mcangle_other1.42.1691066
X-RAY DIFFRACTIONr_scbond_it1.5741.456868
X-RAY DIFFRACTIONr_scbond_other1.573869
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.90716.2031273
X-RAY DIFFRACTIONr_long_range_B_refined3.14216.932041
X-RAY DIFFRACTIONr_long_range_B_other3.14216.9332041
X-RAY DIFFRACTIONr_rigid_bond_restr1.7731704
X-RAY DIFFRACTIONr_sphericity_free19.115150
X-RAY DIFFRACTIONr_sphericity_bonded10.30451760
LS refinement shellResolution: 1.302→1.336 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 150 -
Rwork0.266 2880 -
obs--97.33 %

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