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- PDB-6urk: Barrier-to-autointegration factor soaked in Glycerol: 1 of 14 in ... -

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Basic information

Entry
Database: PDB / ID: 6urk
TitleBarrier-to-autointegration factor soaked in Glycerol: 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: 1.86 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 23, 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

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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
Water2,252125
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)41.790, 41.790, 213.930
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-224-

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.: 125 / 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: 2.32 Å3/Da / Density % sol: 46.94 %
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: 1.86→41.01 Å / Num. obs: 16983 / % possible obs: 99.91 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.75
Reflection shellResolution: 1.86→1.93 Å / Rmerge(I) obs: 1.16 / Num. unique obs: 1634

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 1.86→41.015 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 1697 10 %
Rwork0.1695 15273 -
obs0.175 16970 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.92 Å2 / Biso mean: 40.2406 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 1.86→41.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 18 125 1545
Biso mean--56.26 40.76 -
Num. residues----177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8602-1.91490.33041380.251812461384
1.9149-1.97670.26851380.215612311369
1.9767-2.04740.26181350.21112121347
2.0474-2.12930.26231380.192512551393
2.1293-2.22620.23481380.185512401378
2.2262-2.34360.21961410.172412551396
2.3436-2.49040.23171380.171612561394
2.4904-2.68270.20281410.181712651406
2.6827-2.95260.24181430.17512761419
2.9526-3.37960.21961410.167912771418
3.3796-4.25730.20521480.136513341482
4.2573-41.02470.21771580.164214261584
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)
10.0283-0.0149-0.02440.03630.00430.0169-0.17850.0506-0.1396-0.2493-0.05240.12030.0391-0.0583-0.00010.2917-0.10880.010.2671-0.02550.266416.0741-0.1242-1.6351
20.1020.10260.12560.14560.13880.16640.0358-0.03720.00550.1958-0.05620.00140.4143-0.2254-0.00360.2853-0.09750.04150.2306-0.04440.238915.8638-8.681510.2674
30.06680.02760.00490.0314-0.03370.0964-0.0345-0.0309-0.0709-0.1130.1031-0.12710.05720.0632-0.00020.2477-0.11240.020.2412-0.02250.206422.3982-5.15691.4835
40.14780.130.23540.32760.26220.3929-0.1673-0.0571-0.0114-0.17370.1583-0.2777-0.20130.30880.02040.1439-0.06020.00060.3269-0.03870.25734.92697.01919.492
50.00760.01380.01220.09640.04790.0758-0.04520.0824-0.10740.1273-0.11960.12010.2284-0.1398-0.00020.2304-0.0330.03570.2148-0.02880.232225.2432-0.499318.8526
60.0022-0.00210.0055-0.00370.00010.0136-0.032-0.4178-0.34040.17530.00380.24420.024-0.3198-00.274-0.02930.02710.3358-0.01710.233323.97643.120228.732
70.10970.0864-0.0220.0618-0.01420.028-0.0252-0.18890.09880.05950.11070.0628-0.29330.174-0.00010.2726-0.08680.01940.272-0.05780.233625.630510.897518.9628
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 70 )A28 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 89 )A71 - 89
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 36 )B2 - 36
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 55 )B37 - 55
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 70 )B56 - 70
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 89 )B71 - 89

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