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- PDB-5i2x: Crystal Structure of TPP1 K170del -

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Basic information

Entry
Database: PDB / ID: 5i2x
TitleCrystal Structure of TPP1 K170del
ComponentsAdrenocortical dysplasia protein homolog
KeywordsPROTEIN BINDING / OB fold
Function / homology
Function and homology information


telomere assembly / segmentation / urogenital system development / protection from non-homologous end joining at telomere / telomerase inhibitor activity / establishment of protein localization to telomere / regulation of establishment of protein localization to telomere / shelterin complex / Telomere C-strand synthesis initiation / Telomere C-strand (Lagging Strand) Synthesis ...telomere assembly / segmentation / urogenital system development / protection from non-homologous end joining at telomere / telomerase inhibitor activity / establishment of protein localization to telomere / regulation of establishment of protein localization to telomere / shelterin complex / Telomere C-strand synthesis initiation / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / telomere capping / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / telomerase holoenzyme complex / Removal of the Flap Intermediate from the C-strand / embryonic limb morphogenesis / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / Telomere Extension By Telomerase / telomere maintenance via telomerase / Packaging Of Telomere Ends / DNA polymerase binding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / Inhibition of DNA recombination at telomere / Meiotic synapsis / skeletal system development / intracellular protein transport / DNA Damage/Telomere Stress Induced Senescence / chromosome, telomeric region / nuclear body / protein-containing complex binding / nucleoplasm
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #960 / Adrenocortical dysplasia protein / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Adrenocortical dysplasia protein homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNandakumar, J. / Smith, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R00-CA-167644 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural and functional consequences of a disease mutation in the telomere protein TPP1.
Authors: Bisht, K. / Smith, E.M. / Tesmer, V.M. / Nandakumar, J.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adrenocortical dysplasia protein homolog
B: Adrenocortical dysplasia protein homolog


Theoretical massNumber of molelcules
Total (without water)34,8592
Polymers34,8592
Non-polymers00
Water99155
1
A: Adrenocortical dysplasia protein homolog


Theoretical massNumber of molelcules
Total (without water)17,4291
Polymers17,4291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adrenocortical dysplasia protein homolog


Theoretical massNumber of molelcules
Total (without water)17,4291
Polymers17,4291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.026, 119.026, 170.778
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUARGARGAA93 - 1004 - 11
21LEULEUARGARGBB93 - 1004 - 11
12PROPROGLNGLNAA112 - 12223 - 33
22PROPROGLNGLNBB112 - 12223 - 33
13ALAALATHRTHRAA142 - 15853 - 69
23ALAALATHRTHRBB142 - 15853 - 69
14THRTHRCYSCYSAA176 - 18687 - 97
24THRTHRCYSCYSBB176 - 18687 - 97
15GLUGLUTYRTYRAA200 - 234111 - 145
25GLUGLUTYRTYRBB200 - 234111 - 145

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.88588, 0.326259, 0.329805), (0.435253, 0.338519, 0.834242), (0.160533, 0.882587, -0.441893)39.409519, -25.4779, 22.170719
3given(1), (1), (1)
4given(-0.841133, 0.413485, 0.348606), (0.497808, 0.339993, 0.797867), (0.211382, 0.844651, -0.491815)38.689259, -27.161409, 20.60183
5given(1), (1), (1)
6given(-0.852913, 0.422676, 0.306407), (0.47364, 0.379675, 0.794677), (0.219556, 0.822917, -0.524026)39.12722, -26.010401, 20.319309
7given(1), (1), (1)
8given(-0.857715, 0.400284, 0.322641), (0.474278, 0.373795, 0.797081), (0.198457, 0.83669, -0.510456)39.323711, -26.15597, 21.137659
9given(1), (1), (1)
10given(-0.849114, 0.387236, 0.359241), (0.498855, 0.364329, 0.786389), (0.173636, 0.846943, -0.502531)38.786701, -26.9244, 21.786699

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Components

#1: Protein Adrenocortical dysplasia protein homolog / POT1 and TIN2-interacting protein


Mass: 17429.354 Da / Num. of mol.: 2 / Fragment: OB domain / Mutation: deletion of amino acid K170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACD, PIP1, PTOP, TINT1, TPP1 / Plasmid: pET-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96AP0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 4.34 Å3/Da / Density % sol: 71.65 % / Mosaicity: 0.276 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 3.6 M sodium formate, 100 mM Tris-Cl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.03829 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 16, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03829 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 12617 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.059 / Rrim(I) all: 0.16 / Χ2: 1.496 / Net I/av σ(I): 14.929 / Net I/σ(I): 7.1 / Num. measured all: 86466
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.1170.4851100
3.11-3.2370.3661100
3.23-3.3870.2881100
3.38-3.5670.2121100
3.56-3.7870.171100
3.78-4.076.90.1251100
4.07-4.486.90.11100
4.48-5.136.80.089199.8
5.13-6.466.70.095199.8
6.46-506.20.067197.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I46

2i46


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.897 / SU B: 12.346 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.578 / ESU R Free: 0.312 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 1281 10.2 %RANDOM
Rwork0.192 ---
obs0.1954 11321 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.16 Å2 / Biso mean: 37.111 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.98 Å2
Refinement stepCycle: final / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 0 55 2233
Biso mean---27.87 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192215
X-RAY DIFFRACTIONr_angle_refined_deg0.9881.9873008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3215278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5823.81105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63615367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3341522
X-RAY DIFFRACTIONr_chiral_restr0.0590.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211692
X-RAY DIFFRACTIONr_mcbond_it2.1173.6341124
X-RAY DIFFRACTIONr_mcangle_it3.9395.4171398
X-RAY DIFFRACTIONr_scbond_it1.7143.7981090
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
174MEDIUM POSITIONAL0.50.5
174MEDIUM THERMAL2.942
285MEDIUM POSITIONAL0.380.5
285MEDIUM THERMAL2.962
3122MEDIUM POSITIONAL0.330.5
3122MEDIUM THERMAL4.612
486MEDIUM POSITIONAL0.340.5
486MEDIUM THERMAL3.552
5296MEDIUM POSITIONAL0.510.5
5296MEDIUM THERMAL6.12
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 91 -
Rwork0.275 810 -
all-901 -
obs--100 %

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