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- PDB-3wtd: Structure of PAXX -

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Basic information

Entry
Database: PDB / ID: 3wtd
TitleStructure of PAXX
ComponentsUncharacterized protein C9orf142
KeywordsNUCLEAR PROTEIN / DNA repair / Scaffold
Function / homology
Function and homology information


nonhomologous end joining complex / DNA polymerase binding / double-strand break repair via nonhomologous end joining / site of double-strand break / molecular adaptor activity / DNA damage response / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOchi, T. / Blundell, T.L.
CitationJournal: Science / Year: 2015
Title: DNA repair. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair.
Authors: Ochi, T. / Blackford, A.N. / Coates, J. / Jhujh, S. / Mehmood, S. / Tamura, N. / Travers, J. / Wu, Q. / Draviam, V.M. / Robinson, C.V. / Blundell, T.L. / Jackson, S.P.
History
DepositionApr 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein C9orf142
B: Uncharacterized protein C9orf142


Theoretical massNumber of molelcules
Total (without water)35,7062
Polymers35,7062
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-23 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.948, 91.948, 153.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Uncharacterized protein C9orf142 / PAXX


Mass: 17853.162 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP RESIDUES 1-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C9orf142 / Plasmid: pHAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q9BUH6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5M ammonium sulfate, 12%(v/v) glycerol, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.35→55.2 Å / Num. obs: 16230 / % possible obs: 98.5 % / Redundancy: 9.6 % / Rsym value: 0.052 / Net I/σ(I): 24.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 10 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.627 / % possible all: 99.3

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9pre_1665)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→45.974 Å / SU ML: 0.26 / σ(F): 1.36 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 812 5 %
Rwork0.1934 --
obs0.1952 16225 97.74 %
all-16600 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→45.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 0 97 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082019
X-RAY DIFFRACTIONf_angle_d1.1312763
X-RAY DIFFRACTIONf_dihedral_angle_d13.188728
X-RAY DIFFRACTIONf_chiral_restr0.042319
X-RAY DIFFRACTIONf_plane_restr0.007364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.49730.26181330.22942519X-RAY DIFFRACTION99
2.4973-2.69010.25941330.22432536X-RAY DIFFRACTION99
2.6901-2.96080.25091350.20992566X-RAY DIFFRACTION99
2.9608-3.38910.23691350.19842570X-RAY DIFFRACTION99
3.3891-4.26950.19441360.1832582X-RAY DIFFRACTION98
4.2695-45.98280.23531400.18512640X-RAY DIFFRACTION94
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)
16.5302-3.1363.16157.7981-1.70536.1309-0.1250.00151.2216-0.0344-0.2164-0.7383-0.5579-0.08520.34640.37810.06770.02770.43080.01630.5381-3.9208-31.3805-9.2462
23.4258-3.4894-3.92385.46522.55755.6242-0.1713-0.0259-0.06320.18730.11660.5086-0.0791-0.19690.22520.38010.1269-0.03890.7277-0.01060.4755-10.5697-34.9119-10.7143
37.06851.51311.67336.21422.44493.9915-0.0793-0.46971.0330.3477-0.1681-0.3032-0.82860.08360.18350.4744-0.0601-0.12960.34510.04310.52599.7725-34.9977-0.2226
43.3331-0.46320.86069.4139-3.03196.4934-0.0098-0.68890.00731.036-0.2761-0.1384-0.4899-0.07810.28880.4509-0.1686-0.08220.5580.01020.39115.5125-48.117612.2241
55.3057-3.8148-2.33617.1942-3.35839.17110.47680.39890.64870.5084-0.6059-1.0819-0.3588-0.06080.16890.4225-0.2172-0.1340.58870.03870.426322.0749-44.52598.9839
67.4887-1.81072.17044.7528-0.53664.39310.0565-0.87670.1534-0.14060.090.2137-0.454-0.4755-0.18170.4169-0.07390.03750.44630.01720.18678.8228-41.06466.9147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 5:82 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 83:113 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 114:142 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 5:72 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 73:98 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 99:145 )

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