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- PDB-2ion: Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form2 -

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Basic information

Entry
Database: PDB / ID: 2ion
TitleCrystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form2
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 / MOLECULAR REPLACEMENT / Resolution: 1.57 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: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed Cell Death 4, Pdcd4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6552
Polymers17,5631
Non-polymers921
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.536, 61.536, 78.066
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 17563.117 Da / Num. of mol.: 1 / Fragment: C-terminal MA3 domain, residues 322-450
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): Rosette(DE3)pLysS / References: UniProt: Q61823
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.17 M ammonium sulfate, 0.085 M sodium acetate, 25.5% (w/v) PEG 2000 MME, 15% (v/v) glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.57→30 Å / Num. all: 24343 / Num. obs: 23715 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rsym value: 0.08 / Net I/σ(I): 20.6
Reflection shellResolution: 1.571→1.612 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1605 / Rsym value: 0.501 / % possible all: 95.45

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IOL, Chain A

2iol


Resolution: 1.57→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.251 / SU ML: 0.046 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.069 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 1241 5.1 %RANDOM
Rwork0.15974 ---
all0.183 24343 --
obs0.1615 23008 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.074 Å0.069 Å
Refinement stepCycle: LAST / Resolution: 1.57→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 6 185 1227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221151
X-RAY DIFFRACTIONr_bond_other_d0.0010.021076
X-RAY DIFFRACTIONr_angle_refined_deg1.781.9861578
X-RAY DIFFRACTIONr_angle_other_deg0.96832530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3465157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60524.52853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11815225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.201157
X-RAY DIFFRACTIONr_chiral_restr0.1050.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
X-RAY DIFFRACTIONr_nbd_refined0.2520.2321
X-RAY DIFFRACTIONr_nbd_other0.1750.21144
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2581
X-RAY DIFFRACTIONr_nbtor_other0.0840.2625
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3220.226
X-RAY DIFFRACTIONr_mcbond_it1.5911.5774
X-RAY DIFFRACTIONr_mcbond_other0.3811.5275
X-RAY DIFFRACTIONr_mcangle_it1.88921146
X-RAY DIFFRACTIONr_scbond_it3.0023500
X-RAY DIFFRACTIONr_scangle_it4.5874.5416
LS refinement shellResolution: 1.571→1.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 96 -
Rwork0.329 1605 -
obs--95.45 %

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