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- PDB-1a44: PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN FROM CALF BRAIN -

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Basic information

Entry
Database: PDB / ID: 1a44
TitlePHOSPHATIDYLETHANOLAMINE BINDING PROTEIN FROM CALF BRAIN
ComponentsPHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING / LIPID-BINDING PROTEIN
Function / homologyPhosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein family signature. / MAP2K and MAPK activation / Negative regulation of MAPK pathway / serine-type endopeptidase inhibitor activity / lipid binding ...Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein family signature. / MAP2K and MAPK activation / Negative regulation of MAPK pathway / serine-type endopeptidase inhibitor activity / lipid binding / protein kinase binding / ATP binding / cytoplasm / Phosphatidylethanolamine-binding protein 1
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 1.84 Å resolution
AuthorsSerre, L. / Vallee, B. / Zelwer, C. / Schoentgen, F.
CitationJournal: Structure / Year: 1998
Title: Crystal structure of the phosphatidylethanolamine-binding protein from bovine brain: a novel structural class of phospholipid-binding proteins.
Authors: Serre, L. / Vallee, B. / Bureaud, N. / Schoentgen, F. / Zelwer, C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 10, 1998 / Release: Jan 13, 1999
RevisionDateData content typeGroupProviderType
1.0Jan 13, 1999Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8132
Polyers20,7541
Non-polymers591
Water4,396244
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)82.700, 33.550, 60.070
Angle α, β, γ (deg.)90.00, 97.71, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Protein/peptide PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN / PEBP / PBP


Mass: 20754.363 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / Details: CALF / Genus: Bos / Cellular location: CYTOPLASM / Organ: BRAIN / References: UniProt: P13696
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Formula: C2H3O2 / Acetate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Formula: H2O / Water

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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 / Density percent sol: 38 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
15 mg/mlprotein1drop
210 mMHEPES1drop
32 mMdithiothreitol1drop
420-25 %PEG40001reservoir
50.2 Mammonium acetate1reservoir
60.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: LURE BEAMLINE DW32 / Synchrotron site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorCollection date: Nov 1, 1997
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 9.742 Å2 / D resolution high: 1.84 Å / D resolution low: 36.04 Å / Number obs: 14517 / Observed criterion sigma I: 1 / Rsym value: 0.039 / NetI over sigmaI: 15.8 / Redundancy: 3.3 % / Percent possible obs: 99.8
Reflection shellHighest resolution: 1.84 Å / Lowest resolution: 1.94 Å / MeanI over sigI obs: 8 / Rsym value: 0.093 / Redundancy: 3.3 % / Percent possible all: 98.6
Reflection
*PLUS
Number measured all: 48585 / Rmerge I obs: 0.039
Reflection shell
*PLUS
Rmerge I obs: 0.095

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefineMethod to determine structure: MIR / Cross valid method: RFREE / Sigma F: 0
Displacement parametersB iso mean: 11.89 Å2
Least-squares processR factor R free: 0.216 / R factor R work: 0.148 / Highest resolution: 1.84 Å / Lowest resolution: 36 Å / Number reflection obs: 14517 / Percent reflection R free: 10 / Percent reflection obs: 99.8
Refine hist #LASTHighest resolution: 1.84 Å / Lowest resolution: 36 Å
Number of atoms included #LASTProtein: 1466 / Nucleic acid: 0 / Ligand: 4 / Solvent: 245 / Total: 1715
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0100.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it1.7723.00
X-RAY DIFFRACTIONp_mcangle_it2.3545.00
X-RAY DIFFRACTIONp_scbond_it4.0896.00
X-RAY DIFFRACTIONp_scangle_it5.1708.00
X-RAY DIFFRACTIONp_plane_restr0.0300.04
X-RAY DIFFRACTIONp_chiral_restr0.1310.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.30
X-RAY DIFFRACTIONp_multtor_nbd0.2450.30
X-RAY DIFFRACTIONp_xhyhbond_nbd0.0000.30
X-RAY DIFFRACTIONp_xyhbond_nbd0.1060.30
X-RAY DIFFRACTIONp_planar_tor5.307.00
X-RAY DIFFRACTIONp_staggered_tor15.8015.00
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.2020.00
X-RAY DIFFRACTIONp_special_tor0.0015.00
Software
*PLUS
Name: REFMAC / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.212 / R factor obs: 0.147 / Lowest resolution: 32 Å

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