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- PDB-2iqx: Rat Phosphatidylethanolamine-Binding Protein Containing the S153E... -

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Basic information

Entry
Database: PDB / ID: 2iqx
TitleRat Phosphatidylethanolamine-Binding Protein Containing the S153E Mutation in the Complex with o-Phosphorylethanolamine
ComponentsPhosphatidylethanolamine-binding protein 1
KeywordsHYDROLASE INHIBITOR / alpha-beta
Function / homology
Function and homology information


positive regulation of acetylcholine biosynthetic process / positive regulation of acetylcholine metabolic process / Negative regulation of MAPK pathway / MAP2K and MAPK activation / regulation of the force of heart contraction / receptor serine/threonine kinase binding / mitogen-activated protein kinase binding / sperm capacitation / eating behavior / response to corticosterone ...positive regulation of acetylcholine biosynthetic process / positive regulation of acetylcholine metabolic process / Negative regulation of MAPK pathway / MAP2K and MAPK activation / regulation of the force of heart contraction / receptor serine/threonine kinase binding / mitogen-activated protein kinase binding / sperm capacitation / eating behavior / response to corticosterone / negative regulation of MAPK cascade / spermatid development / positive regulation of cAMP-mediated signaling / axon terminus / response to electrical stimulus / response to cAMP / response to organonitrogen compound / positive regulation of mitotic nuclear division / negative regulation of protein phosphorylation / response to activity / response to organic substance / hippocampus development / serine-type endopeptidase inhibitor activity / response to organic cyclic compound / response to toxic substance / kinase binding / response to calcium ion / MAPK cascade / synaptic vesicle / apical part of cell / response to ethanol / response to oxidative stress / mitochondrial outer membrane / response to xenobiotic stimulus / signaling receptor binding / neuronal cell body / lipid binding / protein kinase binding / enzyme binding / cell surface / extracellular space / ATP binding
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
PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / Phosphatidylethanolamine-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, Y. / Joachimiak, G. / Clark, M.C. / Rosner, M. / Joachimiak, A.
CitationJournal: To be Published
Title: Rat Phosphatidylethanolamine-Binding Crystal structure of Protein Containing the S153E Mutation in the Complex with o-Phosphorylethanolamine
Authors: Kim, Y. / Joachimiak, G. / Clark, M.C. / Rosner, M. / Joachimiak, A.
History
DepositionOct 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylethanolamine-binding protein 1
B: Phosphatidylethanolamine-binding protein 1
C: Phosphatidylethanolamine-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0316
Polymers62,6083
Non-polymers4233
Water10,323573
1
A: Phosphatidylethanolamine-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0102
Polymers20,8691
Non-polymers1411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylethanolamine-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0102
Polymers20,8691
Non-polymers1411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylethanolamine-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0102
Polymers20,8691
Non-polymers1411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.971, 57.211, 80.886
Angle α, β, γ (deg.)90.00, 109.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphatidylethanolamine-binding protein 1 / PEBP-1 / HCNPpp / 23 kDa morphine-binding protein / P23K


Mass: 20869.404 Da / Num. of mol.: 3 / Mutation: S153E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P31044
#2: Chemical ChemComp-OPE / PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / COLAMINE PHOSPHORIC ACID / Phosphorylethanolamine


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


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 277 K / pH: 4.5
Details: 10mM o-phosphorylethamine+ 2mM GTP crystallized in 0.1M Sodium Acetate trihydrate pH 4.5 and 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932
DetectorType: SBC-2 / Detector: CCD / Date: Nov 27, 2003 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.2→32.25 Å / Num. obs: 25715 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 3.1
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 1.8 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BD9

1bd9


Resolution: 2.2→32.24 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.856 / Cross valid method: THROUGHOUT / ESU R: 0.592 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26104 2419 9.8 %RANDOM
Rwork0.18192 ---
obs0.18957 22343 96.35 %-
all-24400 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20.45 Å2
2--0.13 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4367 0 24 573 4964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224511
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9666142
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2965553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1124.857210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47115723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.31521
X-RAY DIFFRACTIONr_chiral_restr0.0860.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023496
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.22346
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2513
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.296
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7651.52783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.46424493
X-RAY DIFFRACTIONr_scbond_it2.4431728
X-RAY DIFFRACTIONr_scangle_it3.9184.51649
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 141
Rwork0.232 1366

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