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- PDB-2qyq: Human raf kinase inhibitor protein (rkip) in complex with o-phosp... -

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Basic information

Entry
Database: PDB / ID: 2qyq
TitleHuman raf kinase inhibitor protein (rkip) in complex with o-phosphotyrosine
ComponentsPhosphatidylethanolamine-binding protein 1
KeywordsSIGNALING PROTEIN INHIBITOR / PROTEIN-LIGAND COMPLEX / CIS-PEPTIDE BONDS
Function / homology
Function and homology information


phosphatidylethanolamine binding / negative regulation of MAPK cascade / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / serine-type endopeptidase inhibitor activity / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions ...phosphatidylethanolamine binding / negative regulation of MAPK cascade / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / serine-type endopeptidase inhibitor activity / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / protein kinase binding / enzyme binding / RNA binding / extracellular exosome / ATP binding / nucleus / cytosol
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
O-PHOSPHOTYROSINE / Phosphatidylethanolamine-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsSimister, P.C. / Brady, R.L.
CitationJournal: Forum Immunopath.Dis.Ther. / Year: 2011
Title: Phosphotyrosine recognition by the Raf Kinase Inhibitor Protein
Authors: Simister, P.C. / Burton, N.M. / Brady, R.L.
History
DepositionAug 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 / 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)21,3482
Polymers21,0871
Non-polymers2611
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.674, 33.892, 59.705
Angle α, β, γ (deg.)90.000, 96.090, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-980-

HOH

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Components

#1: Protein Phosphatidylethanolamine-binding protein 1 / PEBP-1 / Prostatic-binding protein / HCNPpp / Neuropolypeptide h3 / Raf kinase inhibitor protein / RKIP


Mass: 21086.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full-length protein / Source: (gene. exp.) Homo sapiens (human) / Gene: PEBP1, PBP, PEBP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P30086
#2: Chemical ChemComp-PTR / O-PHOSPHOTYROSINE / PHOSPHONOTYROSINE


Type: L-peptide linking / Mass: 261.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Initial crystallisation: 32-34% PEG 4OOO or 8000, 0.2 M sodium acetate, 0.1 M sodium acetate pH 4.0. Complex formed by soaking in: 32% PEG 4OOO, 0.2 M sodium chloride, 0.1 M O- ...Details: Initial crystallisation: 32-34% PEG 4OOO or 8000, 0.2 M sodium acetate, 0.1 M sodium acetate pH 4.0. Complex formed by soaking in: 32% PEG 4OOO, 0.2 M sodium chloride, 0.1 M O-phosphotyrosine, 0.1 M hepes pH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 15, 2003
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.948→59.76 Å / Num. all: 12443 / Num. obs: 11833 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 19.68 Å2 / Rmerge(I) obs: 0.081 / Χ2: 0.998 / Net I/σ(I): 18.2
Reflection shellResolution: 1.948→2.02 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.7 / Num. unique all: 951 / Χ2: 0.693 / % possible all: 78.7

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Phasing

Phasing MRRfactor: 0.381 / Cor.coef. Fo:Fc: 0.609 / Cor.coef. Io to Ic: 0.522
Highest resolutionLowest resolution
Rotation3 Å59.761 Å
Translation3 Å59.761 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEH

1beh


Resolution: 1.948→59.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.754 / SU ML: 0.109 / Isotropic thermal model: ISOTROPIC OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.208 572 4.8 %RANDOM
Rwork0.154 ---
obs0.157 11832 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20.98 Å2
2--0.62 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 1.948→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 17 169 1659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211533
X-RAY DIFFRACTIONr_bond_other_d0.0020.021338
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9642088
X-RAY DIFFRACTIONr_angle_other_deg0.91433132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.075185
X-RAY DIFFRACTIONr_chiral_restr0.1070.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021694
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02302
X-RAY DIFFRACTIONr_nbd_refined0.2020.2278
X-RAY DIFFRACTIONr_nbd_other0.2460.21508
X-RAY DIFFRACTIONr_nbtor_other0.0850.2774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.212
X-RAY DIFFRACTIONr_mcbond_it0.941.5934
X-RAY DIFFRACTIONr_mcangle_it1.59821511
X-RAY DIFFRACTIONr_scbond_it2.5123599
X-RAY DIFFRACTIONr_scangle_it3.8214.5577
LS refinement shellResolution: 1.948→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.302 35
Rwork0.18 614
obs-649

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