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- PDB-1b7a: STRUCTURE OF THE PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN FROM BO... -

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Basic information

Entry
Database: PDB / ID: 1b7a
TitleSTRUCTURE OF THE PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN FROM BOVINE BRAIN
ComponentsPHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / PHOSPHOLIPID BINDING PROTEIN
Function / homology
Function and homology information


MAP2K and MAPK activation / Negative regulation of MAPK pathway / negative regulation of MAPK cascade / serine-type endopeptidase inhibitor activity / lipid binding / ATP binding / cytoplasm
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
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / Phosphatidylethanolamine-binding protein 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSerre, L. / Vallee, B. / Bureaud, N. / Schoentgen, F. / Zelwer, C.
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.
History
DepositionJan 21, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0494
Polymers41,7672
Non-polymers2822
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.200, 77.160, 107.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.97096, -0.23875, -0.01506), (-0.23266, 0.92782, 0.29157), (-0.05564, 0.28661, -0.95643)
Vector: 57.20056, -2.06845, 59.80603)

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Components

#1: Protein PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN / PEBP


Mass: 20883.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: BRAIN / References: UniProt: P13696
#2: Chemical ChemComp-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID


Mass: 141.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8NO4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE OPE MOLECULES HAVE TWO CONFORMATIONS
Sequence detailsGLY: THE SIDE CHAIN OF THE C-TERMINAL LYS186 WAS NOT SEEN I THE ELECTRON DENSITY MAP AND WAS ...GLY: THE SIDE CHAIN OF THE C-TERMINAL LYS186 WAS NOT SEEN I THE ELECTRON DENSITY MAP AND WAS REFINED AS GLYCINE.

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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: 2.18 Å3/Da / Density % sol: 44 %
Crystal growpH: 4.3
Details: 25-27% PEG8000, 100 MM PHOSPHORYLETHANOLAMINE, pH 4.3
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2PEG 800012
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 mMHEPES1drop
32 mMdithiothreitol1drop
425-27 %PEG80001reservoir
5100 mMphosphorylethanolamine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→29 Å / Num. obs: 16450 / % possible obs: 90.8 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 4.9 / Net I/σ(I): 12.4
Reflection shellResolution: 2.25→2.41 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 7.1 / Rsym value: 10.6 / % possible all: 88.8

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A44

1a44


Resolution: 2.25→12.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1625 10 %RANDOM
Rwork0.208 ---
all-16289 --
obs-16289 90 %-
Displacement parametersBiso mean: 24.37 Å2
Refinement stepCycle: LAST / Resolution: 2.25→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 32 164 3145
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0420.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8552
X-RAY DIFFRACTIONp_mcangle_it2.7993
X-RAY DIFFRACTIONp_scbond_it2.4932
X-RAY DIFFRACTIONp_scangle_it3.8313
X-RAY DIFFRACTIONp_plane_restr0.0338
X-RAY DIFFRACTIONp_chiral_restr0.140.15
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2580.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.27
X-RAY DIFFRACTIONp_staggered_tor1715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.820
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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