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- PDB-6urn: Barrier-to-autointegration factor t-butanol: 1 of 14 in MSCS set -

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Basic information

Entry
Database: PDB / ID: 6urn
TitleBarrier-to-autointegration factor t-butanol: 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: 1.68 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
Water2,630146
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)41.690, 41.690, 214.190
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.: 146 / 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: 46.75 %
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: 1.68→38.85 Å / Num. obs: 22716 / % possible obs: 99.86 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.21
Reflection shellResolution: 1.68→1.74 Å / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 2211

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 1.68→40.922 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 1999 8.8 %
Rwork0.1697 20711 -
obs0.1728 22710 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.66 Å2 / Biso mean: 37.7781 Å2 / Biso min: 16.19 Å2
Refinement stepCycle: final / Resolution: 1.68→40.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1402 0 18 146 1566
Biso mean--57.9 41.41 -
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 (%)
1.68-1.7220.30151380.26721419155799
1.722-1.76860.33081380.229214291567100
1.7686-1.82060.2591380.21814461584100
1.8206-1.87940.24721390.203914411580100
1.8794-1.94660.2521400.195514491589100
1.9466-2.02450.26071410.196314541595100
2.0245-2.11670.22651410.176314591600100
2.1167-2.22820.19071400.174714521592100
2.2282-2.36780.18581430.161314731616100
2.3678-2.55060.21131420.159514731615100
2.5506-2.80730.21351450.168415061651100
2.8073-3.21330.17761460.168515111657100
3.2133-4.04790.18161480.151615251673100
4.0479-40.93420.19421600.161216741834100
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)
10.03890.0616-0.0214-0.01930.06410.1044-0.20970.12720.0763-0.32870.15630.20390.02990.00200.2917-0.1322-0.01760.270.00070.267516.31030.1739-1.5735
20.28480.23970.38780.39240.46070.60370.0295-0.04120.00160.1762-0.03370.01170.4511-0.2277-0.00350.2745-0.10340.0330.2331-0.02070.231216.2072-8.39310.239
30.02850.05110.0720.0808-0.14310.2778-0.10940.119-0.1163-0.17630.119-0.09250.05770.1217-0.00040.2534-0.12920.03150.2581-0.0320.236722.6366-4.84261.4419
40.19560.05210.1310.3730.19230.3502-0.1606-0.0101-0.0532-0.07410.223-0.2169-0.20860.3740.01430.1336-0.0595-0.00370.3148-0.03580.240335.02276.207119.9389
50.03280.00190.05090.04840.16160.2571-0.0803-0.1243-0.0610.13420.00830.06620.2409-0.006-00.1797-0.01820.02190.2433-0.02540.208124.84280.555817.6704
60.04260.05040.07730.0087-0.01080.0975-0.0096-0.2707-0.14070.1496-0.11760.0579-0.109-0.037500.1789-0.0190.01930.351-0.02510.201924.41473.205228.6861
70.10480.11510.01340.1882-0.09380.0732-0.041-0.1581-0.02750.02720.2341-0.0258-0.2967-0.02310.00580.2084-0.09050.01130.2776-0.05540.224126.061211.101818.7804
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 37 )B2 - 37
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 55 )B38 - 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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