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- PDB-1beh: HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CA... -

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Basic information

Entry
Database: PDB / ID: 1beh
TitleHUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CACODYLATE
ComponentsPHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING / SIGNALLING
Function / homology
Function and homology information


phosphatidylethanolamine binding / negative regulation of MAPK cascade / serine-type endopeptidase inhibitor activity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 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 / serine-type endopeptidase inhibitor activity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / 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, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Phosphatidylethanolamine-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBanfield, M.J. / Barker, J.J. / Perry, A. / 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 14, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
B: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4484
Polymers42,1742
Non-polymers2742
Water4,306239
1
A: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2242
Polymers21,0871
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2242
Polymers21,0871
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.430, 61.630, 67.920
Angle α, β, γ (deg.)90.00, 101.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.48316, 0.87203, -0.07827), (0.87452, -0.48497, -0.00483), (-0.04217, -0.06611, -0.99692)
Vector: 8.7598, -8.39688, 86.06371)

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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: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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
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: Apr 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: 1.7→20 Å / Num. obs: 38803 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / % possible all: 94.9
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BD9

1bd9


Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1773 5 %SHELLS
Rwork0.235 ---
obs-33851 95 %-
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 10 239 3168
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.12
X-RAY DIFFRACTIONp_mcangle_it1.63
X-RAY DIFFRACTIONp_scbond_it1.22
X-RAY DIFFRACTIONp_scangle_it1.93
X-RAY DIFFRACTIONp_plane_restr0.0210.03
X-RAY DIFFRACTIONp_chiral_restr0.1110.15
X-RAY DIFFRACTIONp_singtor_nbd0.1720.3
X-RAY DIFFRACTIONp_multtor_nbd0.2390.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor15.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2220
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.83 Å / Rfactor all: 0.268 / Rfactor obs: 0.322

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