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- PDB-9xzt: Crystal structure of BBn6 -

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Basic information

Entry
Database: PDB / ID: 9xzt
TitleCrystal structure of BBn6
ComponentsBBn6
KeywordsDE NOVO PROTEIN / de novo design / parametric / beta-barrel / sequence-structure relation ship / machine learning / nanopore
Function / homologyChem-PG6
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsBera, A.K. / Kim, D. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Parametrically guided design of beta barrels and transmembrane nanopores using deep learning.
Authors: Kim, D.E. / Watson, J.L. / Juergens, D. / Majumder, S. / Sonigra, R. / Gerben, S.R. / Kang, A. / Bera, A.K. / Li, X. / Baker, D.
History
DepositionAug 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BBn6
B: BBn6
C: BBn6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3407
Polymers30,5893
Non-polymers7514
Water1,02757
1
A: BBn6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4632
Polymers10,1961
Non-polymers2661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BBn6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2922
Polymers10,1961
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BBn6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5853
Polymers10,1961
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.190, 74.190, 97.635
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein BBn6


Mass: 10196.434 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M AmSO4, 30%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.03→53.67 Å / Num. obs: 20674 / % possible obs: 99.5 % / Redundancy: 13.5 % / Biso Wilson estimate: 50.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.029 / Net I/σ(I): 14.27
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 13 % / Rmerge(I) obs: 2.21 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 1442 / CC1/2: 0.644 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→38.87 Å / SU ML: 0.3217 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.5281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2653 2005 9.72 %
Rwork0.2193 18629 -
obs0.2237 20634 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.16 Å2
Refinement stepCycle: LAST / Resolution: 2.03→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 38 57 2165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222143
X-RAY DIFFRACTIONf_angle_d0.50222850
X-RAY DIFFRACTIONf_chiral_restr0.0455288
X-RAY DIFFRACTIONf_plane_restr0.0042372
X-RAY DIFFRACTIONf_dihedral_angle_d13.0473829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.38561400.3291317X-RAY DIFFRACTION99.86
2.08-2.140.35491400.27761297X-RAY DIFFRACTION99.93
2.14-2.20.33111420.27071306X-RAY DIFFRACTION99.86
2.2-2.270.32481420.24871332X-RAY DIFFRACTION100
2.27-2.350.30121390.25611298X-RAY DIFFRACTION100
2.35-2.450.30641420.24831313X-RAY DIFFRACTION99.93
2.45-2.560.29461410.2641341X-RAY DIFFRACTION100
2.56-2.690.34521440.23281300X-RAY DIFFRACTION100
2.69-2.860.30251400.26281333X-RAY DIFFRACTION100
2.86-3.080.30981430.24591321X-RAY DIFFRACTION100
3.08-3.390.31951400.23441341X-RAY DIFFRACTION100
3.39-3.880.24441450.20011337X-RAY DIFFRACTION100
3.88-4.890.18941500.16621366X-RAY DIFFRACTION99.93
4.89-38.870.27291570.22931427X-RAY DIFFRACTION99.94
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)
12.61751129772-0.3564006157080.3184809560874.758910547260.07488582335754.598654650830.123969061166-0.2513274233940.1397446014050.378939271753-0.05432901192150.0650059755594-0.277768248875-0.315375848762-0.06858348021630.4221695314540.01480734225680.04470503579940.407967488064-0.006176821213050.411872808317.11305788356-24.59330418581.80174156137
23.199452109610.8954386315870.5669102524525.056492028050.7322204136222.463876777860.0983649442813-0.1975452963620.0818904160604-0.0356751323505-0.1990135171230.208338724310.026325417959-0.4049805426410.06680214790580.404835157710.02881366249820.02190609438910.479926963068-0.04156387717890.389336889383-4.09025101234-29.6013864065-14.2896449139
32.912285995550.547259166824-0.04570498613943.4157815817-0.1955669253274.80544257570.0651680302545-0.497167672935-0.4786546663710.164593287336-0.179109192504-0.2381399005160.3413427751780.7548200939280.1742063354190.4832199836910.1759789018190.01947881701820.60163548130.08779871869790.54875983063531.9358904225-40.8869656384-8.97265761676
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 1 - 90 / Label seq-ID: 1 - 90

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain A and resseq 1:90)AA
22(chain B and resseq 1:90)BB
33(chain C and resseq 1:90)CC

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