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- PDB-2ios: Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); ... -

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Basic information

Entry
Database: PDB / ID: 2ios
TitleCrystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form 3
ComponentsProgrammed Cell Death 4, Pdcd4
KeywordsANTITUMOR PROTEIN / alpha-helical
Function / homology
Function and homology information


epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / response to alkaloid / positive regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / response to alkaloid / positive regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of cytokine production involved in inflammatory response / BMP signaling pathway / response to hormone / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / negative regulation of DNA-templated transcription / apoptotic process / negative regulation of apoptotic process / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Programmed cell death protein 4 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsWlodawer, A. / LaRonde-LeBlanc, N.A.
CitationJournal: Mol.Cell.Biol. / Year: 2007
Title: Structural basis for inhibition of translation by the tumor suppressor pdcd4.
Authors: Laronde-Leblanc, N. / Santhanam, A.N. / Baker, A.R. / Wlodawer, A. / Colburn, N.H.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed Cell Death 4, Pdcd4


Theoretical massNumber of molelcules
Total (without water)17,3511
Polymers17,3511
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.254, 64.021, 38.453
Angle α, β, γ (deg.)90.00, 114.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-39-

HOH

21A-76-

HOH

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Components

#1: Protein Programmed Cell Death 4, Pdcd4 / / Pdcd4


Mass: 17350.844 Da / Num. of mol.: 1 / Fragment: C-terminal MA3 domain, residues 323-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd4, MA-3 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q61823
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10% (w/v) PEG-3000, 100 mM phosphate-citrate, 200 mM NaCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.76→30 Å / Num. all: 15015 / Num. obs: 14854 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rsym value: 0.033 / Net I/σ(I): 32.2
Reflection shellResolution: 1.76→1.806 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.54 / Num. unique all: 1034 / Rsym value: 0.248 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IOL, chain A.

2iol


Resolution: 1.76→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.584 / SU ML: 0.085 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24853 754 5 %RANDOM
Rwork0.19459 ---
all0.212 15015 --
obs0.19718 14183 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.106 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0.88 Å2
2---0.23 Å20 Å2
3----0.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.126 Å0.119 Å
Refinement stepCycle: LAST / Resolution: 1.76→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 0 116 1129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221036
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9821406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.71824.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62915185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.654154
X-RAY DIFFRACTIONr_chiral_restr0.1150.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02758
X-RAY DIFFRACTIONr_nbd_refined0.2460.2543
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.210
X-RAY DIFFRACTIONr_mcbond_it1.5781.5653
X-RAY DIFFRACTIONr_mcangle_it2.23321034
X-RAY DIFFRACTIONr_scbond_it3.6133428
X-RAY DIFFRACTIONr_scangle_it5.5344.5370
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 45 -
Rwork0.262 989 -
obs--95.56 %

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