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- PDB-6ent: Structure of the rat RKIP variant delta143-146 -

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Basic information

Entry
Database: PDB / ID: 6ent
TitleStructure of the rat RKIP variant delta143-146
ComponentsPhosphatidylethanolamine-binding protein 1
KeywordsSIGNALING PROTEIN / RKIP / PEBP / PBP
Function / homology
Function and homology information


positive regulation of acetylcholine biosynthetic process / positive regulation of acetylcholine metabolic process / 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 / eating behavior / response to corticosterone ...positive regulation of acetylcholine biosynthetic process / positive regulation of acetylcholine metabolic process / 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 / eating behavior / response to corticosterone / negative regulation of MAPK cascade / spermatid development / positive regulation of cAMP-mediated signaling / axon terminus / response to electrical stimulus / response to cAMP / response to organonitrogen compound / positive regulation of mitotic nuclear division / negative regulation of protein phosphorylation / response to activity / response to organic substance / hippocampus development / serine-type endopeptidase inhibitor activity / response to organic cyclic compound / response to toxic substance / kinase binding / response to calcium ion / MAPK cascade / synaptic vesicle / apical part of cell / response to ethanol / response to oxidative stress / mitochondrial outer membrane / response to xenobiotic stimulus / signaling receptor binding / neuronal cell body / lipid binding / protein kinase binding / enzyme 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 / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Phosphatidylethanolamine-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsKoelmel, W. / Hirschbeck, M. / 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.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _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 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylethanolamine-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3143
Polymers21,2131
Non-polymers1012
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-36 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.250, 111.250, 111.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

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Components

#1: Protein Phosphatidylethanolamine-binding protein 1 / PEBP-1 / 23 kDa morphine-binding protein / HCNPpp / P23K / Raf Kinase Inhibitory Protein


Mass: 21212.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pebp1, Pbp, Pebp / Production host: Escherichia coli (E. coli) / References: UniProt: P31044
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium fluoride

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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: Sep 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.66→55.63 Å / Num. obs: 6706 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.7
Reflection shellResolution: 2.66→2.81 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.465 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ENS

6ens


Resolution: 2.66→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 31.629 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 0.849 / ESU R Free: 0.322 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25043 315 4.7 %RANDOM
Rwork0.20959 ---
obs0.21148 6365 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 86.067 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 2 6 1404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191473
X-RAY DIFFRACTIONr_bond_other_d0.0020.021343
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.942013
X-RAY DIFFRACTIONr_angle_other_deg0.92333117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8342470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37615230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.142157
X-RAY DIFFRACTIONr_chiral_restr0.0780.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211677
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02342
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_it1.7695.64716
X-RAY DIFFRACTIONr_mcbond_other1.7695.635715
X-RAY DIFFRACTIONr_mcangle_it3.0478.437896
X-RAY DIFFRACTIONr_mcangle_other3.0458.443897
X-RAY DIFFRACTIONr_scbond_it1.3525.792757
X-RAY DIFFRACTIONr_scbond_other1.3515.796758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3718.6451116
X-RAY DIFFRACTIONr_long_range_B_refined4.78564.9721586
X-RAY DIFFRACTIONr_long_range_B_other4.78365.0191587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.664→2.732 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 21 -
Rwork0.306 432 -
obs--99.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4529-0.48134.71590.1832-1.662615.7633-0.1026-0.23990.10670.10740.05480.0477-0.6754-0.58980.04790.3216-0.06060.14390.3961-0.04370.4304-34.984124.438131.8924
25.9262-0.63441.31896.3193-2.64163.90430.1746-0.18080.0047-0.27530.07030.11270.2875-0.2173-0.24490.0622-0.0475-0.090.0410.07340.1609-32.377810.842928.6565
35.00296.7385-2.66569.2306-3.70041.50390.04420.27150.06690.12310.27090.443-0.0325-0.1235-0.31510.6689-0.1086-0.14950.6109-0.04610.9709-47.6711-1.135226.5991
41.1508-2.22721.58795.3862-0.35039.10220.34920.0655-0.1651-0.5193-0.27560.34420.8898-0.2778-0.07360.32660.06380.00340.05730.0110.4722-26.09550.887926.7151
57.7616-2.97321.7993.8735-0.16674.10320.20830.7912-0.8054-0.628-0.09750.25940.86-0.0145-0.11080.3956-0.1332-0.10520.17250.04170.3769-34.75893.271423.7053
67.77631.65720.76930.8905-0.26890.4726-0.09260.3145-0.1745-0.01890.12010.02090.0646-0.0956-0.02740.37640.0266-0.00710.30670.00610.3598-28.7163-6.474232.5434
70.34740.81360.75136.7975-2.35955.48060.1735-0.0155-0.05870.0908-0.02150.19930.69230.1284-0.1520.12290.0087-0.03550.08160.12320.2211-32.85111.539835.4442
80.18770.0244-0.19132.30414.2778.255-0.17280.24-0.1545-0.10940.0512-0.06760.0371-0.15120.12160.5023-0.1056-0.02110.492-0.05470.4806-42.38175.39259.3971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 4
2X-RAY DIFFRACTION2A5 - 70
3X-RAY DIFFRACTION3A71 - 83
4X-RAY DIFFRACTION4A84 - 96
5X-RAY DIFFRACTION5A97 - 126
6X-RAY DIFFRACTION6A127 - 146
7X-RAY DIFFRACTION7A147 - 167
8X-RAY DIFFRACTION8A168 - 176

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