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- PDB-3wtf: Structure of PAXX -

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Basic information

Entry
Database: PDB / ID: 3wtf
TitleStructure of PAXX
ComponentsUncharacterized protein C9orf142
KeywordsIMMUNE SYSTEM / 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: 3.451 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 1.2Nov 8, 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

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Assembly

Deposited unit
A: Uncharacterized protein C9orf142
B: Uncharacterized protein C9orf142


Theoretical massNumber of molelcules
Total (without water)43,6152
Polymers43,6152
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-25 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.576, 89.576, 151.404
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: 21807.629 Da / Num. of mol.: 2
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 / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1M sodium malonate, 1% (v/v) 1,4-Dioxane, pH 6.0, 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: 3.45→24.47 Å / Num. obs: 4986 / % possible obs: 97.3 % / Redundancy: 6.1 % / Rsym value: 0.088 / Net I/σ(I): 9.1
Reflection shellResolution: 3.45→3.78 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 1150 / Rsym value: 0.599 / % possible all: 98.2

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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
Starting model: 3WTD

3wtd


Resolution: 3.451→24.47 Å / SU ML: 0.52 / σ(F): 1.34 / Phase error: 35.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 492 10.01 %Random
Rwork0.2349 ---
obs0.2385 4916 96.17 %-
all-5111 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.451→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 0 3 1812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121853
X-RAY DIFFRACTIONf_angle_d1.6422550
X-RAY DIFFRACTIONf_dihedral_angle_d12.071621
X-RAY DIFFRACTIONf_chiral_restr0.072306
X-RAY DIFFRACTIONf_plane_restr0.01335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.451-3.79710.41811190.3657105796
3.7971-4.34390.33291210.2853109698
4.3439-5.46290.3091220.2579110997
5.4629-24.47080.22191300.1969116294
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)
14.3645-3.5793-0.90563.73781.07850.30260.27850.039-0.3991-0.4532-0.2626-0.21560.40080.3244-0.10831.8439-0.04930.08621.7587-0.06941.6404-42.8303109.6115143.6024
26.0732-2.59110.71054.43030.42612.1572-0.0539-0.18170.07620.76480.1020.2442-0.0988-0.25570.05021.5279-0.14740.15972.0079-0.06151.5921-59.9095121.7032160.7362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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