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- PDB-2iqy: Rat Phosphatidylethanolamine-Binding Protein -

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Basic information

Entry
Database: PDB / ID: 2iqy
TitleRat Phosphatidylethanolamine-Binding Protein
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
Phosphatidylethanolamine-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKim, Y. / Joachimiak, G. / Heil, G.L. / Koide, S. / Joachimiak, A.
CitationJournal: To be Published
Title: Crystal Structure of Rat Phosphatidylethanolamine-Binding Protein
Authors: Kim, Y. / Joachimiak, G. / Heil, G.L. / Koide, S. / 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 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylethanolamine-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1753
Polymers21,1001
Non-polymers762
Water7,242402
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.694, 70.588, 38.672
Angle α, β, γ (deg.)90.00, 109.96, 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: 21099.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P31044
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Cacl2, HEPES pH 7.5 and 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97932
DetectorType: SBC-3 / Detector: CCD / Date: Oct 6, 2006 / 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: 1.4→26.23 Å / Num. all: 28140 / Num. obs: 28140 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.6
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 7.45 / Num. unique all: 1510 / % possible all: 48.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IQX

2iqx


Resolution: 1.4→26.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19299 2838 10.1 %RANDOM
Rwork0.14879 ---
all0.15321 25281 --
obs0.15321 25281 89.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.07 Å2
2--0.26 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.4→26.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 2 402 2090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211748
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9652408
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71825.42283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60215298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.947158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021429
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2640.21031
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2371
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0490.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.295
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8211.51089
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36321792
X-RAY DIFFRACTIONr_scbond_it1.9693659
X-RAY DIFFRACTIONr_scangle_it2.7994.5616
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.228 117
Rwork0.171 971
obs-971

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