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- PDB-6us7: Barrier-to-autointegration factor soaked in TMAO: 1 of 14 in MSCS set -

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Basic information

Entry
Database: PDB / ID: 6us7
TitleBarrier-to-autointegration factor soaked in TMAO: 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 / 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 / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation ...negative regulation of protein ADP-ribosylation / Nuclear Envelope Breakdown / mitotic nuclear membrane reassembly / Initiation of Nuclear Envelope (NE) Reformation / 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 / negative regulation of cGAS/STING signaling pathway / 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

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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
Water3,189177
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)41.940, 41.940, 213.880
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 / 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.: 177 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
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→39.04 Å / Num. obs: 24073 / % possible obs: 99.92 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.54
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 2325

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 1.653→39.045 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1982 2000 8.31 %
Rwork0.1601 22063 -
obs0.1632 24063 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.37 Å2 / Biso mean: 32.7408 Å2 / Biso min: 14.67 Å2
Refinement stepCycle: final / Resolution: 1.653→39.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 18 177 1597
Biso mean--49.33 38.81 -
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 (%)
1.653-1.69440.26051380.230715271665100
1.6944-1.74020.25671410.205915491690100
1.7402-1.79140.21741380.193515151653100
1.7914-1.84920.24091390.189815351674100
1.8492-1.91530.21121410.187815701711100
1.9153-1.9920.22981410.177715451686100
1.992-2.08270.21731380.183615311669100
2.0827-2.19240.21021410.172815601701100
2.1924-2.32980.21111430.157415811724100
2.3298-2.50960.20651410.157415511692100
2.5096-2.76210.22211450.160215891734100
2.7621-3.16170.18971450.155616031748100
3.1617-3.98280.16611480.143416371785100
3.9828-39.05550.18371610.14631770193199
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)
10.09850.0367-0.05110.0372-0.03650.1022-0.06040.0712-0.041-0.1933-0.06060.1795-0.0551-0.0753-0.03540.237-0.1129-0.00390.2089-0.01080.220616.0997-0.1474-1.6458
20.074-0.0882-0.00750.2170.04290.22630.1041-0.2986-0.22560.2711-0.24150.2369-0.105-0.1347-0.01820.2771-0.16370.08090.3453-0.06930.27726.0755-8.20069.952
30.05570.07550.13570.09410.17320.1697-0.02320.0258-0.01610.15190.0170.05620.2554-0.1043-00.2058-0.05380.01420.1702-0.02740.212720.4442-3.980711.8252
40.06610.07450.03980.09910.00190.17240.12990.0764-0.13210.10020.0134-0.04390.7409-0.24340.03220.374-0.08940.00340.1653-0.02110.222817.6195-14.548.6015
50.10660.00130.19880.0729-0.16740.2831-0.0296-0.0032-0.00780.04490.05180.070.05190.12220.0050.2075-0.10690.0260.1837-0.02710.180622.5037-5.12241.4532
60.24280.149-0.07010.38960.09070.1397-0.2019-0.0935-0.001-0.07960.2567-0.2163-0.17050.34890.01310.1347-0.0454-0.00410.2841-0.03850.215234.75746.012220.0106
70.0460.0790.11870.14430.11090.1657-0.0345-0.1262-0.04440.1719-0.0112-0.05150.161-0.0753-00.1771-0.05150.01980.219-0.02290.19424.54870.388817.738
80.02960.03710.06810.0391-0.04030.0798-0.1078-0.4934-0.26790.34070.05870.1073-0.0691-0.176-0.00010.2335-0.03540.02870.3122-0.00950.197524.04363.186728.7173
90.18150.1394-0.09280.1149-0.0430.0666-0.115-0.11730.0945-0.0170.09070.0122-0.25210.09360.00020.1996-0.08520.01580.2287-0.04370.178525.811810.966818.7501
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 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 37 )B2 - 37
7X-RAY DIFFRACTION7chain 'B' and (resid 38 through 55 )B38 - 55
8X-RAY DIFFRACTION8chain 'B' and (resid 56 through 70 )B56 - 70
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 89 )B71 - 89

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