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- PDB-6us0: Barrier-to-autointegration factor soaked in R,S,R-bisfuranol (RSR... -

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Basic information

Entry
Database: PDB / ID: 6us0
TitleBarrier-to-autointegration factor soaked in R,S,R-bisfuranol (RSR): 1 of 14 in MSCS set
ComponentsBarrier-to-autointegration factor
KeywordsDNA BINDING PROTEIN / alpha helical / MSCS / minor groove binder
Function / homology
Function and homology information


negative regulation of protein ADP-ribosylation / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / negative regulation of cGAS/STING signaling pathway / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of type I interferon production / negative regulation of viral genome replication / 2-LTR circle formation ...negative regulation of protein ADP-ribosylation / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / negative regulation of cGAS/STING signaling pathway / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / negative regulation of type I interferon production / negative regulation of viral genome replication / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / chromosome organization / condensed chromosome / negative regulation of innate immune response / response to virus / DNA integration / nuclear envelope / chromatin organization / double-stranded DNA binding / response to oxidative stress / chromatin / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Barrier- to-autointegration factor, BAF / Barrier-to-autointegration factor, BAF superfamily / : / Barrier to autointegration factor / Barrier to autointegration factor
Similarity search - Domain/homology
ETHANOL / Barrier-to-autointegration factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.653 Å
AuthorsAgarwal, S. / Smith, M. / De La Rosa, I. / Kliment, A.V. / Swartz, P. / Segura-Totten, M. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor.
Authors: Agarwal, S. / Smith, M. / De La Rosa, I. / Verba, K.A. / Swartz, P. / Segura-Totten, M. / Mattos, C.
History
DepositionOct 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Barrier-to-autointegration factor
B: Barrier-to-autointegration factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2394
Polymers20,1472
Non-polymers922
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.710, 41.710, 214.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

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Components

#1: Protein Barrier-to-autointegration factor / Breakpoint cluster region protein 1


Mass: 10073.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BANF1, BAF, BCRG1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75531
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 80 mM Tris pH 8.5, 16% Ethanol, 10% PEG-1450

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→32.92 Å / Num. obs: 23877 / % possible obs: 99.9 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.16
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.48 / Num. unique obs: 2311

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 1.653→40.942 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 1998 8.37 %
Rwork0.1623 21869 -
obs0.1655 23867 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.78 Å2 / Biso mean: 35.4658 Å2 / Biso min: 15.28 Å2
Refinement stepCycle: final / Resolution: 1.653→40.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 18 172 1592
Biso mean--52.37 40.71 -
Num. residues----177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.653-1.69440.26841390.220715161655100
1.6944-1.74020.24161410.206115421683100
1.7402-1.79140.26941360.199414951631100
1.7914-1.84920.24311390.194715191658100
1.8492-1.91530.24731400.19815421682100
1.9153-1.9920.25871410.182715361677100
1.992-2.08270.25481410.189415341675100
2.0827-2.19250.21051400.181715441684100
2.1925-2.32980.20151410.164115481689100
2.3298-2.50970.18041420.161915461688100
2.5097-2.76220.20211440.163515801724100
2.7622-3.16170.19381440.156115841728100
3.1617-3.98290.18211490.149216251774100
3.9829-40.95470.18241610.14361758191999
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)
10.0381-0.0156-0.02990.04770.03740.0414-0.18860.18220.0552-0.4460.08610.246-0.0777-0.0633-0.00040.2842-0.1423-0.01960.25970.00310.241216.1568-0.0172-1.5862
20.1366-0.1031-0.0150.10150.01530.0838-0.1967-0.1125-0.27030.2715-0.12540.1859-0.09780.0046-0.03620.3187-0.31180.10550.3491-0.12840.24536.1416-8.09619.9473
30.05470.08580.11720.08180.11440.3524-0.0053-0.02620.08340.07360.0460.0180.4038-0.13580.00310.2582-0.07750.02190.1794-0.02710.192319.2423-8.733210.4033
40.03650.03230.04230.0577-0.0480.15960.02520.0019-0.0482-0.06590.0142-0.02060.02820.20530.01450.233-0.15270.03050.2332-0.03680.18522.5491-4.89121.4301
50.20380.17420.07680.65310.29060.3349-0.1781-0.0557-0.0254-0.22190.195-0.3079-0.19720.50470.01430.1142-0.0401-0.01310.3149-0.03960.2334.81926.090620.0129
60.02970.03650.06380.05540.06780.0858-0.1103-0.0742-0.07160.13050.01950.03260.2804-0.1089-00.1833-0.02480.02030.2273-0.03210.206924.64030.435717.7282
70.00810.02460.03130.0311-0.0290.0447-0.1169-0.412-0.13370.1383-0.04070.0972-0.143-0.14680.00050.2358-0.03230.02860.3332-0.03030.198524.1973.193428.6959
80.1564-0.0629-0.01490.1497-0.05850.0434-0.1231-0.18170.0743-0.00810.16770.0807-0.1718-0.06290.00480.2073-0.09130.0060.2804-0.04050.198925.869111.001118.7915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )A1 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 37 )A28 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 70 )A38 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 89 )A71 - 89
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 37 )B2 - 37
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 55 )B38 - 55
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 70 )B56 - 70
8X-RAY DIFFRACTION8chain 'B' and (resid 71 through 89 )B71 - 89

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