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- PDB-1bd9: HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1bd9
TitleHUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
ComponentsPHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING / SIGNALLING
Function / homology
Function and homology information


phosphatidylethanolamine binding / negative regulation of MAPK cascade / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / serine-type endopeptidase inhibitor activity / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions ...phosphatidylethanolamine binding / negative regulation of MAPK cascade / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / serine-type endopeptidase inhibitor activity / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / protein kinase binding / enzyme binding / RNA binding / extracellular exosome / ATP binding / nucleus / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.05 Å
AuthorsBanfield, M.J. / Barker, J.J. / Perry, A.C.F. / Brady, R.L.
CitationJournal: Structure / Year: 1998
Title: Function from structure? The crystal structure of human phosphatidylethanolamine-binding protein suggests a role in membrane signal transduction.
Authors: Banfield, M.J. / Barker, J.J. / Perry, A.C. / Brady, R.L.
History
DepositionMay 12, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)42,1742
Polymers42,1742
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.420, 60.740, 67.640
Angle α, β, γ (deg.)90.00, 102.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.50466, -0.86269, -0.03312), (-0.86321, -0.50362, -0.03505), (0.01355, 0.04628, -0.99884)
Vector: 23.26832, 39.15271, 112.53713)

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Components

#1: Protein PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN


Mass: 21086.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM, MEMBRANE-ASSOCIATED / Plasmid: PET-15B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30086
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.2 Å3/Da / Density % sol: 36 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE, PH 6.5; THEN SOAKED IN 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM BIS-TRIS, PH 6.5.
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein11can be replaced by 10mg/ml
25 mMBis-Tris11
30.01 %sodium azide11
428-32 %PEG400012can be replaced by PEG6000 or PEG8000
5200-300 mMsodium acetate12
60.01 %sodium azide12
7100 mMsodium cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: MIRRORS
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 23495 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.3
Reflection shellResolution: 2.05→2.14 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 9.8 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.05→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1147 5 %SHELLS
Rwork0.171 ---
obs-22684 100 %-
Displacement parametersBiso mean: 15.5 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 0 394 3302
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0240.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0282
X-RAY DIFFRACTIONp_mcangle_it1.4723
X-RAY DIFFRACTIONp_scbond_it1.2862
X-RAY DIFFRACTIONp_scangle_it1.9453
X-RAY DIFFRACTIONp_plane_restr0.0210.03
X-RAY DIFFRACTIONp_chiral_restr0.110.15
X-RAY DIFFRACTIONp_singtor_nbd0.1690.3
X-RAY DIFFRACTIONp_multtor_nbd0.2410.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.87
X-RAY DIFFRACTIONp_staggered_tor13.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.720
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 2.15 Å / Rfactor Rfree: 0.23 / Rfactor obs: 0.161

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