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- PDB-2vge: Crystal structure of the C-terminal region of human iASPP -

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Basic information

Entry
Database: PDB / ID: 2vge
TitleCrystal structure of the C-terminal region of human iASPP
ComponentsRELA-ASSOCIATED INHIBITOR
KeywordsTRANSCRIPTION / IASPP / NUCLEUS / APOPTOSIS / REPRESSOR / CYTOPLASM / PHOSPHORYLATION / P53 BINDING PROTEIN / ANK REPEAT / SH3 DOMAIN / ANKYRIN REPEATS / ALTERNATIVE SPLICING / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


multicellular organismal-level homeostasis / cardiac right ventricle morphogenesis / embryonic camera-type eye development / hair cycle / ventricular cardiac muscle tissue development / Regulation of TP53 Activity through Association with Co-factors / intercellular bridge / cardiac muscle contraction / post-embryonic development / positive regulation of cell differentiation ...multicellular organismal-level homeostasis / cardiac right ventricle morphogenesis / embryonic camera-type eye development / hair cycle / ventricular cardiac muscle tissue development / Regulation of TP53 Activity through Association with Co-factors / intercellular bridge / cardiac muscle contraction / post-embryonic development / positive regulation of cell differentiation / multicellular organism growth / transcription corepressor activity / cell junction / cadherin binding / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
RelA-associated inhibitor / RelA-associated inhibitor, SH3 domain / Variant SH3 domain / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...RelA-associated inhibitor / RelA-associated inhibitor, SH3 domain / Variant SH3 domain / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
RelA-associated inhibitor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRobinson, R.A. / Lu, X. / Jones, E.Y. / Siebold, C.
CitationJournal: Structure / Year: 2008
Title: Biochemical and Structural Studies of Aspp Proteins Reveal Differential Binding to P53, P63 and P73
Authors: Robinson, R.A. / Lu, X. / Jones, E.Y. / Siebold, C.
History
DepositionNov 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RELA-ASSOCIATED INHIBITOR


Theoretical massNumber of molelcules
Total (without water)25,3141
Polymers25,3141
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.969, 67.545, 50.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2116-

HOH

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Components

#1: Protein RELA-ASSOCIATED INHIBITOR / INHIBITOR OF ASPP PROTEIN / PROTEIN IASPP / PPP1R13B-LIKE PROTEIN / NFKB-INTERACTING PROTEIN 1 / IASPP


Mass: 25314.373 Da / Num. of mol.: 1 / Fragment: P53 (CORE) BINDING DOMAIN, RESIDUES 607-828
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET 22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) PLYSS / References: UniProt: Q8WUF5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.09 Å3/Da / Density % sol: 40.73 % / Description: NONE
Crystal growDetails: 22% PEG3350, 0.3 M KCL2, 17.5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.97566
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97566 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 12454 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YCS

1ycs


Resolution: 2.1→29.43 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 219304.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 587 5.1 %RANDOM
Rwork0.208 ---
obs0.208 11554 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.9959 Å2 / ksol: 0.361446 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.16 Å20 Å20 Å2
2--8.64 Å20 Å2
3----2.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 0 153 1745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.392
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 79 4.7 %
Rwork0.33 1600 -
obs--82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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