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- PDB-6d0l: Structure of human TIRR -

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Basic information

Entry
Database: PDB / ID: 6d0l
TitleStructure of human TIRR
ComponentsTudor-interacting repair regulator protein
KeywordsPROTEIN BINDING / RNA binding / NUDT16L1 / 53BP1 / DNA damage response / DNA double-strand break repair
Function / homology
Function and homology information


negative regulation of double-strand break repair via nonhomologous end joining / snoRNA binding / RNA binding / nucleus
Similarity search - Function
: / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tudor-interacting repair regulator protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsCui, G. / Botuyan, M.V. / Mer, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM116829 United States
Department of Defense (DOD, United States)W81XWH-16-1-0391 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Mechanism of 53BP1 activity regulation by RNA-binding TIRR and a designer protein.
Authors: Botuyan, M.V. / Cui, G. / Drane, P. / Oliveira, C. / Detappe, A. / Brault, M.E. / Parnandi, N. / Chaubey, S. / Thompson, J.R. / Bragantini, B. / Zhao, D. / Chapman, J.R. / Chowdhury, D. / Mer, G.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tudor-interacting repair regulator protein
B: Tudor-interacting repair regulator protein


Theoretical massNumber of molelcules
Total (without water)46,0782
Polymers46,0782
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-25 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.890, 46.360, 48.800
Angle α, β, γ (deg.)92.31, 108.07, 105.75
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tudor-interacting repair regulator protein / NUDT16-like protein 1 / Protein syndesmos


Mass: 23038.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16L1, SDOS, TIRR / Plasmid: pBB75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BRJ7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 1.86 Å3/Da / Density % sol: 34.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.06 M citric acid, 0.04 M Bis-Tris-Propane, pH 4.1, 16% PEG 3,350; Cryoprotection in 25% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→38 Å / Num. obs: 22070 / % possible obs: 93.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.17 Å2 / Rmerge(I) obs: 0.0837 / Rrim(I) all: 0.09815 / Net I/σ(I): 15.12
Reflection shellResolution: 1.97→2.041 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.3381 / Mean I/σ(I) obs: 5.15 / Num. unique obs: 1980 / Rrim(I) all: 0.3956 / % possible all: 84.07

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KVH

3kvh


Resolution: 1.97→38 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2091 1104 5.01 %
Rwork0.1742 --
obs0.176 22048 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3048 0 0 351 3399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063257
X-RAY DIFFRACTIONf_angle_d0.714431
X-RAY DIFFRACTIONf_dihedral_angle_d11.3521217
X-RAY DIFFRACTIONf_chiral_restr0.044505
X-RAY DIFFRACTIONf_plane_restr0.005566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9702-2.05990.2641270.21272409X-RAY DIFFRACTION86
2.0599-2.16850.27141340.20992530X-RAY DIFFRACTION92
2.1685-2.30430.27451370.20152604X-RAY DIFFRACTION92
2.3043-2.48220.22281390.18322633X-RAY DIFFRACTION95
2.4822-2.7320.23151400.18142673X-RAY DIFFRACTION95
2.732-3.12710.20011410.17262674X-RAY DIFFRACTION96
3.1271-3.93920.18011410.14922679X-RAY DIFFRACTION96
3.9392-380.1671450.15752742X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5243-0.5570.5243.15961.23021.8259-0.0331-0.137-0.09170.29710.2547-0.43460.24240.1169-0.25290.28630.036-0.09160.3735-0.12080.244918.204-14.972346.1584
21.7641-0.41640.1731.12860.55340.87580.0094-0.04910.058-0.03180.0226-0.0473-0.01040.0549-0.01130.0402-0.01880.01910.1086-0.01520.10656.9159-15.567129.7571
35.60630.28441.44254.3752-0.1924.33630.0356-0.4115-0.48860.1957-0.1259-0.41280.520.37530.00930.18680.03110.07970.27-0.00410.18213.4956-17.153241.5303
41.0235-0.1809-0.15581.68710.37930.7858-0.0152-0.0317-0.02270.06670.01050.09650.077-0.00950.00740.0536-0.02040.01130.0944-0.01430.0680.3096-24.841331.7452
51.22490.0925-1.4080.59330.39612.0682-0.40950.1638-0.2765-0.59460.01360.1742-0.0533-0.07110.06890.4768-0.0503-0.00470.6326-0.40470.6411-12.9197-48.71656.4609
62.6723-0.28630.83622.25680.26852.43250.11070.02950.00110.0631-0.128-0.22630.03950.199-0.00460.1267-0.0014-0.00320.1675-0.0190.07928.9284-32.532811.711
70.6735-0.1106-0.03850.53710.01710.50810.26310.4207-0.2262-0.2303-0.13590.31370.2239-0.3750.0413-0.291-0.0480.02440.3442-0.06840.1789-6.709-32.809313.5095
83.87690.81122.05764.86630.1712.8482-0.07850.496-0.25190.0554-0.09070.3578-0.1363-0.54750.16950.1379-0.0579-0.02190.3955-0.12950.2894-8.4049-36.54186.1407
91.2939-0.09940.40371.37820.26571.8574-0.03810.1568-0.0667-0.0784-0.05690.064-0.0768-0.10630.04340.0785-0.02310.01360.1188-0.03520.09124.1562-33.021414.6941
105.243-0.1862-0.49234.8160.46957.10910.0633-0.6104-0.09340.54720.1405-0.12440.08370.4442-0.11440.125-0.02240.00160.12980.01660.18689.8994-43.266930.1274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 107 )
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 210 )
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 46 )
7X-RAY DIFFRACTION7chain 'B' and (resid 47 through 73 )
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 107 )
9X-RAY DIFFRACTION9chain 'B' and (resid 108 through 184 )
10X-RAY DIFFRACTION10chain 'B' and (resid 185 through 208 )

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