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- PDB-2xvs: Crystal structure of human TTC5 (Strap) C-terminal OB domain -

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Basic information

Entry
Database: PDB / ID: 2xvs
TitleCrystal structure of human TTC5 (Strap) C-terminal OB domain
ComponentsTETRATRICOPEPTIDE REPEAT PROTEIN 5
KeywordsANTITUMOR PROTEIN / P53 COFACTOR / STRESS-RESPONSE / P300
Function / homology
Function and homology information


positive regulation of mRNA catabolic process / cellular response to starvation / Regulation of TP53 Activity through Methylation / ribosome binding / cytoplasmic vesicle / mitochondrial matrix / DNA repair / DNA damage response / chromatin binding / positive regulation of transcription by RNA polymerase II ...positive regulation of mRNA catabolic process / cellular response to starvation / Regulation of TP53 Activity through Methylation / ribosome binding / cytoplasmic vesicle / mitochondrial matrix / DNA repair / DNA damage response / chromatin binding / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / cytosol
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #550 / Tetratricopeptide repeat protein 5, OB fold domain / TTC5, OB fold domain superfamily / Tetratricopeptide repeat protein 5 OB fold domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Tetratricopeptide-like helical domain superfamily ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #550 / Tetratricopeptide repeat protein 5, OB fold domain / TTC5, OB fold domain superfamily / Tetratricopeptide repeat protein 5 OB fold domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Tetratricopeptide-like helical domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Tetratricopeptide repeat protein 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAdams, J. / Pike, A.C.W. / Maniam, S. / Sharpe, T.D. / Coutts, A.S. / Knapp, S. / La Thangue, B. / Bullock, A.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: The P53 Cofactor Strap Exhibits an Unexpected Tpr Motif and Oligonucleotide-Binding (Ob)-Fold Structure.
Authors: Adams, C.J. / Pike, A.C. / Maniam, S. / Sharpe, T.D. / Coutts, A.S. / Knapp, S. / La Thangue, N.B. / Bullock, A.N.
History
DepositionOct 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references / Structure summary
Revision 1.2Mar 21, 2012Group: Other
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: TETRATRICOPEPTIDE REPEAT PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6606
Polymers18,1821
Non-polymers4785
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.260, 62.390, 78.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TETRATRICOPEPTIDE REPEAT PROTEIN 5 / TPR REPEAT PROTEIN 5 / STRAP


Mass: 18182.023 Da / Num. of mol.: 1 / Fragment: OLIGONUCLEOTIDE-BINDING DOMAIN, RESIDUES 262-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q8N0Z6
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / 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: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 8.5
Details: 0.18M SODIUM IODIDE, 0.02M SODIUM ACETATE, 20% PEG3350, 10% ETHYLENE GLYCOL, 0.45% DMSO, 0.1M BIS-TRIS-PROPANE PH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.8→33.3 Å / Num. obs: 14246 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→78.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.787 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23638 723 5.1 %RANDOM
Rwork0.17242 ---
obs0.1755 13521 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.906 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→78.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 8 116 1361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221283
X-RAY DIFFRACTIONr_bond_other_d0.0020.02864
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9971742
X-RAY DIFFRACTIONr_angle_other_deg2.00932133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9445167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1124.37548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90115219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.447157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02236
X-RAY DIFFRACTIONr_nbd_refined0.2110.2207
X-RAY DIFFRACTIONr_nbd_other0.1850.2826
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2607
X-RAY DIFFRACTIONr_nbtor_other0.0930.2639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2393829
X-RAY DIFFRACTIONr_mcbond_other0.9743337
X-RAY DIFFRACTIONr_mcangle_it4.43851336
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0078454
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.36111405
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free16.48334
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 58 -
Rwork0.259 803 -
obs--84.08 %
Refinement TLS params.Method: refined / Origin x: 1.9395 Å / Origin y: -4.0812 Å / Origin z: -3.7795 Å
111213212223313233
T0.011 Å20.008 Å20.0113 Å2-0.0164 Å20.0273 Å2--0.0608 Å2
L2.8531 °20.7711 °2-0.2091 °2-3.1681 °2-1.3651 °2--2.3567 °2
S0.0603 Å °0.1698 Å °0.3037 Å °0.085 Å °0.0397 Å °0.1471 Å °-0.1543 Å °-0.0763 Å °-0.1 Å °

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