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- PDB-1kn3: Murine PEBP-2 (phosphatidylethanolamine-binding protein-2) -

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Basic information

Entry
Database: PDB / ID: 1kn3
TitleMurine PEBP-2 (phosphatidylethanolamine-binding protein-2)
ComponentsPhosphatidylethanolamine Binding Protein-2
KeywordsPROTEIN BINDING / Phosphatidylethanolamine binding / Raf-1 kinase inhibitor / Cis-peptide
Function / homology
Function and homology information


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
Phosphatidylethanolamine-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSimister, P.C. / Banfield, M.J. / Brady, R.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The crystal structure of PEBP-2, a homologue of the PEBP/RKIP family.
Authors: Simister, P.C. / Banfield, M.J. / Brady, R.L.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 2023Group: 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-2


Theoretical massNumber of molelcules
Total (without water)20,7781
Polymers20,7781
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.816, 51.401, 79.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphatidylethanolamine Binding Protein-2 / mPEBP-2


Mass: 20777.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: pebp-2 / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8VIN1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 200mM sodium acetate trihydrate, 100mM Tris.HCl, pH 8.5, VAPOUR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein11
220 mMBis-Tris11
3100 mM11pH6.NaCl
430 %PEG400012
5200 mMsodium acetate trihydrate12
6100 mMTris-HCl12pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2001 / Details: Mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 16223 / Num. obs: 15638 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.084
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 3.26 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 8.5 / % possible all: 92.4
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 92.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.116

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BD9

1bd9


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.926 / SU B: 3.94 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26667 801 5.1 %Random
Rwork0.21043 ---
all0.21315 14777 --
obs0.21315 14777 96.5 %-
Displacement parametersBiso mean: 13.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 123 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211484
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9472023
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2013179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41315256
X-RAY DIFFRACTIONr_chiral_restr0.1050.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021143
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.3682
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.5168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.330
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7571.5901
X-RAY DIFFRACTIONr_mcangle_it1.13521462
X-RAY DIFFRACTIONr_scbond_it1.9813583
X-RAY DIFFRACTIONr_scangle_it3.084.5561
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.923 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.243 139 -
Rwork0.221 2561 -
obs-2561 94.5 %
Refinement TLS params.Method: refined / Origin x: 10.3695 Å / Origin y: 22.7567 Å / Origin z: 11.8122 Å
111213212223313233
T0.0545 Å20.0212 Å2-0.0282 Å2-0.0498 Å2-0.0206 Å2--0.0169 Å2
L2.2223 °2-0.3801 °20.1449 °2-2.8388 °20.289 °2--1.445 °2
S0.0871 Å °0.1771 Å °-0.0747 Å °-0.2599 Å °-0.13 Å °0.2094 Å °-0.0336 Å °-0.1396 Å °0.0429 Å °
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Rfactor all: 0.21315 / Rfactor obs: 0.21 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.49
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.22 / Rfactor obs: 0.22

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