[English] 日本語
Yorodumi
- PDB-3wtf: Structure of PAXX -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more