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- PDB-8uzl: Designed Transmembrane beta-barrel- TMB10_163 -

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Basic information

Entry
Database: PDB / ID: 8uzl
TitleDesigned Transmembrane beta-barrel- TMB10_163
ComponentsDesigned Transmembrane beta-barrel TMB10_163
KeywordsDE NOVO PROTEIN / Computational design / nanopore / TMB
Function / homologyHEXANE-1,6-DIOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBera, A.K. / Lemma, S.B. / Kang, A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2024
Title: Sculpting conducting nanopore size and shape through de novo protein design.
Authors: Berhanu, S. / Majumder, S. / Muntener, T. / Whitehouse, J. / Berner, C. / Bera, A.K. / Kang, A. / Liang, B. / Khan, N. / Sankaran, B. / Tamm, L.K. / Brockwell, D.J. / Hiller, S. / Radford, S. ...Authors: Berhanu, S. / Majumder, S. / Muntener, T. / Whitehouse, J. / Berner, C. / Bera, A.K. / Kang, A. / Liang, B. / Khan, N. / Sankaran, B. / Tamm, L.K. / Brockwell, D.J. / Hiller, S. / Radford, S.E. / Baker, D. / Vorobieva, A.A.
History
DepositionNov 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed Transmembrane beta-barrel TMB10_163
B: Designed Transmembrane beta-barrel TMB10_163
C: Designed Transmembrane beta-barrel TMB10_163
D: Designed Transmembrane beta-barrel TMB10_163
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9906
Polymers65,7534
Non-polymers2362
Water1,78399
1
A: Designed Transmembrane beta-barrel TMB10_163


Theoretical massNumber of molelcules
Total (without water)16,4381
Polymers16,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Designed Transmembrane beta-barrel TMB10_163


Theoretical massNumber of molelcules
Total (without water)16,4381
Polymers16,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Designed Transmembrane beta-barrel TMB10_163


Theoretical massNumber of molelcules
Total (without water)16,4381
Polymers16,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Designed Transmembrane beta-barrel TMB10_163
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6753
Polymers16,4381
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.628, 52.552, 100.050
Angle α, β, γ (deg.)90.000, 93.675, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Designed Transmembrane beta-barrel TMB10_163


Mass: 16438.357 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 3.25M 1,6 Hexanediol and 0.01 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.5→55.51 Å / Num. obs: 38215 / % possible obs: 98.87 % / Redundancy: 4.3 % / Biso Wilson estimate: 43.07 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1255 / Rpim(I) all: 0.06884 / Net I/σ(I): 4.26
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.9234 / Mean I/σ(I) obs: 0.36 / Num. unique obs: 1961 / CC1/2: 0.832 / Rpim(I) all: 0.4931 / % possible all: 98.54

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→55.51 Å / SU ML: 0.4064 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 33.0968
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2621 1661 4.35 %
Rwork0.2272 36554 -
obs0.2288 38215 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.26 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 16 99 4535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00154526
X-RAY DIFFRACTIONf_angle_d0.43986191
X-RAY DIFFRACTIONf_chiral_restr0.047737
X-RAY DIFFRACTIONf_plane_restr0.0038779
X-RAY DIFFRACTIONf_dihedral_angle_d10.58171626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.41061380.33673058X-RAY DIFFRACTION98.34
2.57-2.660.35861100.32163089X-RAY DIFFRACTION98.31
2.66-2.750.39011090.28923099X-RAY DIFFRACTION98.4
2.75-2.860.34531700.26713051X-RAY DIFFRACTION98.56
2.86-2.990.29951850.25462972X-RAY DIFFRACTION98.41
2.99-3.150.31931310.22853094X-RAY DIFFRACTION97.61
3.15-3.350.21761110.22573091X-RAY DIFFRACTION98.07
3.35-3.610.24631160.2073021X-RAY DIFFRACTION97.36
3.61-3.970.25021560.22743061X-RAY DIFFRACTION97.31
3.97-4.540.26321140.18972969X-RAY DIFFRACTION94.77
4.54-5.720.22741780.19082984X-RAY DIFFRACTION97.83
5.72-55.510.21321430.23323065X-RAY DIFFRACTION97.92
Refinement TLS params.Method: refined / Origin x: 24.5429548895 Å / Origin y: 14.999064831 Å / Origin z: 24.8839351405 Å
111213212223313233
T0.273885303513 Å20.0318208863082 Å20.0114009996891 Å2-0.201884231239 Å2-0.00324764010136 Å2--0.235730083832 Å2
L-0.0418518085421 °20.0319398392274 °20.00410167732351 °2--0.0352385400603 °20.0470821035161 °2--0.346199424704 °2
S0.0201178300371 Å °0.0247621801208 Å °-0.00783860801767 Å °0.0266214064571 Å °-0.0101266960529 Å °0.0193563914436 Å °0.0331740344999 Å °-0.0126715462423 Å °-1.31026141474E-8 Å °
Refinement TLS groupSelection details: all

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