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- PDB-6unt: Barrier-to-autointegration factor soaked in DMSO: 1 of 14 in MSCS set -

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Basic information

Entry
Database: PDB / ID: 6unt
TitleBarrier-to-autointegration factor soaked in DMSO: 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: 1.75 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 13, 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 / _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
Water2,720151
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)41.770, 41.770, 213.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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 / 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.: 151 / 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: 46.81 %
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: 277.15 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: 1.75→71.21 Å / Num. obs: 20320 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Net I/σ(I): 13.7 / Num. measured all: 276443 / Scaling rejects: 1376
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.075 / Num. unique obs: 1075 / CC1/2: 0.788 / Rpim(I) all: 0.297 / Rrim(I) all: 1.116 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementResolution: 1.75→40.994 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 1999 9.89 %
Rwork0.1661 18212 -
obs0.1715 20211 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.28 Å2 / Biso mean: 34.8395 Å2 / Biso min: 13.42 Å2
Refinement stepCycle: final / Resolution: 1.75→40.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 18 151 1564
Biso mean--51.47 37.79 -
Num. residues----177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.79380.28711390.238812641403
1.7938-1.84230.31661370.241912551392
1.8423-1.89650.271410.233112801421
1.8965-1.95770.2741370.250712491386
1.9577-2.02770.24241410.193612841425
2.0277-2.10890.24191410.188912801421
2.1089-2.20480.23591400.171212751415
2.2048-2.32110.19911410.171812911432
2.3211-2.46650.19331420.163112911433
2.4665-2.65690.24361400.160412751415
2.6569-2.92420.24021450.169813171462
2.9242-3.34710.21541450.161113271472
3.3471-4.21640.20351490.130513641513
4.2164-41.00480.20481610.156614601621
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)
10.1177-0.1-0.00790.08480.01610.08310.01020.0756-0.3055-0.3161-0.09240.27870.0372-0.07180.00480.3065-0.1202-0.04510.2276-0.01840.286118.1626-1.8297-6.8739
20.10290.00970.02110.08630.11410.1169-0.1306-0.03370.1566-0.0607-0.10390.13940.0112-0.2283-0.10560.2161-0.14790.04470.2494-0.04820.238210.6039-2.84256.2203
30.050.05490.06960.05330.07030.0757-0.10610.06930.00160.23340.04470.07130.2361-0.121-0.00060.1791-0.06340.02720.1618-0.0360.185720.4389-3.940911.8418
40.17510.0616-0.32050.0492-0.15650.68160.03250.1029-0.20820.09810.0054-0.10180.6171-0.32770.01140.3783-0.0942-0.00760.1734-0.01910.24617.5973-14.448.6548
5-0.00060.0263-0.01220.0673-0.07930.11550.1035-0.02230.017-0.0259-0.06030.0530.06640.21580.00580.0771-0.34420.02840.0381-0.06060.194522.4007-4.95111.4916
60.00470.0108-0.00830.1691-0.13940.1226-0.1256-0.07470.0921-0.0946-0.0334-0.2748-0.0212-0.0115-0.00920.1816-0.0937-0.02410.2354-0.03210.232633.482616.086817.9887
70.05390.0225-0.01340.20410.10310.0537-0.09840.0449-0.082-0.09960.1804-0.3025-0.11110.31420.0070.1129-0.0421-0.00320.3239-0.04810.243435.25671.753620.7865
80.02750.02560.01680.03910.06340.1182-0.0109-0.0025-0.14670.1447-0.07210.00980.0862-0.0121-00.1625-0.03380.01650.215-0.03220.190424.54840.421317.6995
90.00810.00370.01910.01340.00710.0356-0.1637-0.3623-0.27890.18470.04660.1304-0.1441-0.14800.214-0.03090.0320.3151-0.03090.205824.06243.144528.6768
100.07260.063-0.00730.0404-0.01530.0252-0.0307-0.08930.11660.00460.09990.0452-0.13830.144900.1892-0.07980.02160.2482-0.04630.170825.915810.998518.8954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )A1 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 37 )A12 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 55 )A38 - 55
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 70 )A56 - 70
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 89 )A71 - 89
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 11 )B2 - 11
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 37 )B12 - 37
8X-RAY DIFFRACTION8chain 'B' and (resid 38 through 55 )B38 - 55
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 70 )B56 - 70
10X-RAY DIFFRACTION10chain 'B' and (resid 71 through 89 )B71 - 89

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