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- PDB-2r77: Crystal structure of phosphatidylethanolamine-binding protein, pf... -

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Basic information

Entry
Database: PDB / ID: 2r77
TitleCrystal structure of phosphatidylethanolamine-binding protein, pfl0955c, from Plasmodium falciparum
ComponentsPhosphatidylethanolamine-binding protein, putative
KeywordsLIPID BINDING PROTEIN / plasmodium falciparum malaria lipid phosphatidylethanolamine / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Negative regulation of MAPK pathway / phosphatidylethanolamine binding / protein kinase regulator activity
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
Raf kinase inhibitor
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsWernimont, A.K. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Sun, X. / Khuu, C. / Crombette, L. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. ...Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Sun, X. / Khuu, C. / Crombette, L. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D. / Xiao, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of phosphatidylethanolamine-binding protein, pfl0955c, from Plasmodium falciparum.
Authors: Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Sun, X. / Khuu, C. / Crombette, L. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / ...Authors: Wernimont, A.K. / Lew, J. / Kozieradzki, I. / Lin, Y.H. / Sun, X. / Khuu, C. / Crombette, L. / Zhao, Y. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D. / Xiao, T.
History
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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, putative


Theoretical massNumber of molelcules
Total (without water)23,5181
Polymers23,5181
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.229, 54.229, 69.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
DetailsAuthors state that the biological unit of this protein is experimentally unknown

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Components

#1: Protein Phosphatidylethanolamine-binding protein, putative


Mass: 23517.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFL0955c / Plasmid: p15-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: Q7KQK1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 3350, 0.2 M Sodium chloride, 0.1 M Sodium cacodylate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 22535 / Num. obs: 22535 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.055 / Rsym value: 0.041 / Χ2: 2.066 / Net I/σ(I): 19.4
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.83 / Num. unique all: 1363 / Rsym value: 0.378 / Χ2: 1.602 / % possible all: 56.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.62 Å
Translation2.5 Å33.62 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GZQ

2gzq


Resolution: 1.65→33.61 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.213 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1163 5.2 %RANDOM
Rwork0.185 ---
obs0.187 22535 92.28 %-
all-22535 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.364 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 0 243 1752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221562
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9582124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6385194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28424.78369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61715268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.643155
X-RAY DIFFRACTIONr_chiral_restr0.10.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021184
X-RAY DIFFRACTIONr_nbd_refined0.2060.2715
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.330.220
X-RAY DIFFRACTIONr_mcbond_it0.8221.5982
X-RAY DIFFRACTIONr_mcangle_it1.31921563
X-RAY DIFFRACTIONr_scbond_it2.0063657
X-RAY DIFFRACTIONr_scangle_it3.1164.5558
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 52 -
Rwork0.431 905 -
all-957 -
obs-1363 54.16 %

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