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- PDB-5vl4: Accidental minimum contact crystal lattice formed by a redesigned... -

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Basic information

Entry
Database: PDB / ID: 5vl4
TitleAccidental minimum contact crystal lattice formed by a redesigned protein oligomer
ComponentsT33-53H-B
KeywordsDE NOVO PROTEIN / BIONANOTECHNOLOGY / SYMMETRY / BIOMATERIALS / COMPUTATIONAL DESIGN / ROSETTA / SELF-ASSEMBLY / NANOMATERIAL / SOLUBILITY
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsCannon, K.A. / Cascio, D. / Sawaya, M.R. / Park, R. / Boyken, S. / King, N. / Yeates, T.
CitationJournal: Protein Sci. / Year: 2020
Title: Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering.
Authors: Cannon, K.A. / Park, R.U. / Boyken, S.E. / Nattermann, U. / Yi, S. / Baker, D. / King, N.P. / Yeates, T.O.
History
DepositionApr 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 2, 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_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
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T33-53H-B


Theoretical massNumber of molelcules
Total (without water)21,0291
Polymers21,0291
Non-polymers00
Water00
1
A: T33-53H-B
x 24


Theoretical massNumber of molelcules
Total (without water)504,70124
Polymers504,70124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
crystal symmetry operation3_554-x,y+1/2,-z-1/21
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_545z+1/2,-x-1/2,-y1
crystal symmetry operation7_455-z-1/2,-x,y+1/21
crystal symmetry operation8_554-z,x+1/2,-y-1/21
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_554-y,z+1/2,-x-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
crystal symmetry operation13_455x-1/2,y+1/2,z+1/21
crystal symmetry operation14_545-x,-y-1/2,z1
crystal symmetry operation15_455-x-1/2,y,-z1
crystal symmetry operation16_554x,-y,-z-1/21
crystal symmetry operation17_455z-1/2,x+1/2,y+1/21
crystal symmetry operation18_554z,-x,-y-1/21
crystal symmetry operation19_545-z,-x-1/2,y1
crystal symmetry operation20_455-z-1/2,x,-y1
crystal symmetry operation21_455y-1/2,z+1/2,x+1/21
crystal symmetry operation22_455-y-1/2,z,-x1
crystal symmetry operation23_554y,-z,-x-1/21
crystal symmetry operation24_545-y,-z-1/2,x1
Unit cell
Length a, b, c (Å)138.380, 138.380, 138.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

#1: Protein T33-53H-B


Mass: 21029.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Plasmid: pET29b / Production host: Escherichia coli (E. coli)

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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: 5.25 Å3/Da / Density % sol: 76.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Na citrate pH 5.6, 2.5M 1,6-hexanediol, 0.01M manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.1→97.85 Å / Num. obs: 3554 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.992 % / Biso Wilson estimate: 135.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.162 / Χ2: 0.742 / Net I/σ(I): 6.57 / Num. measured all: 21295 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.1-4.24.9830.7762.312400.7420.86594.9
4.2-4.326.1440.6483.062570.8640.70899.6
4.32-4.456.1250.5323.642550.9010.58299.6
4.45-4.586.1260.4674.262390.8850.51299.6
4.58-4.736.0750.4484.252130.890.49198.6
4.73-4.95.9480.4044.742330.8970.44399.6
4.9-5.086.060.3724.862150.9330.40898.2
5.08-5.295.810.3475.142100.9230.38298.1
5.29-5.535.1910.3344.661990.9440.37199.5
5.53-5.86.1510.3954.611920.910.43399.5
5.8-6.116.2710.3635.051920.9440.39699.5
6.11-6.486.2650.2466.931700.9530.269100
6.48-6.936.2080.158.921680.9890.16399.4
6.93-7.486.3580.11711.251510.990.127100
7.48-8.25.490.10911.891510.990.1298.7
8.2-9.166.7440.09614.481290.9920.104100
9.16-10.586.5770.09714.731110.9920.10599.1
10.58-12.966.2770.07415.471010.9940.08199
12.96-18.335.6080.07914.52790.9910.08897.5
18.33-97.856.1020.06415.684910.07894.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NOG

1nog


Resolution: 4.1→97.85 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.837 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.612
RfactorNum. reflection% reflectionSelection details
Rfree0.264 355 10 %RANDOM
Rwork0.21 ---
obs0.215 3551 99 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 267.24 Å2 / Biso min: 209.82 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: final / Resolution: 4.1→97.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 0 0 1179
Num. residues----149
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d437SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes172HARMONIC5
X-RAY DIFFRACTIONt_it1195HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion159SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1536SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1195HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg1614HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion23.24
LS refinement shellResolution: 4.1→4.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3242 99 10 %
Rwork0.2792 891 -
all0.2839 990 -
obs--98.9 %
Refinement TLS params.Method: refined / Origin x: -32.2601 Å / Origin y: -18.1027 Å / Origin z: -12.0729 Å
111213212223313233
T-0.1781 Å2-0.0459 Å20.0892 Å2-0.084 Å20.1678 Å2--0.2918 Å2
L1.728 °21.3039 °2-3.8645 °2-3.9771 °2-1.0559 °2--4.2493 °2
S0.0033 Å °0.0099 Å °0.0201 Å °-0.0143 Å °0.058 Å °0.101 Å °-0.1104 Å °0.0272 Å °-0.0613 Å °
Refinement TLS groupSelection details: { A|* }

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