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- PDB-7rmx: Structure of De Novo designed tunable symmetric protein pockets -

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Basic information

Entry
Database: PDB / ID: 7rmx
TitleStructure of De Novo designed tunable symmetric protein pockets
ComponentsTunable symmetric protein, D_3_212
KeywordsDE NOVO PROTEIN / De novo DESIGN / tunable / symmetric protein / pockets
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBera, A.K. / Hicks, D.R. / Kang, A. / Sankaran, B. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: De novo design of protein homodimers containing tunable symmetric protein pockets.
Authors: Hicks, D.R. / Kennedy, M.A. / Thompson, K.A. / DeWitt, M. / Coventry, B. / Kang, A. / Bera, A.K. / Brunette, T.J. / Sankaran, B. / Stoddard, B. / Baker, D.
History
DepositionJul 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: 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 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Tunable symmetric protein, D_3_212


Theoretical massNumber of molelcules
Total (without water)26,5641
Polymers26,5641
Non-polymers00
Water1,72996
1
A: Tunable symmetric protein, D_3_212

A: Tunable symmetric protein, D_3_212


Theoretical massNumber of molelcules
Total (without water)53,1282
Polymers53,1282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3370 Å2
ΔGint-14 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.091, 97.212, 36.266
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Tunable symmetric protein, D_3_212


Mass: 26563.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 20000, glycerol, sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine, MES/imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 25328 / % possible obs: 99.04 % / Redundancy: 7.7 % / Biso Wilson estimate: 25.92 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.59
Reflection shellResolution: 1.64→1.7 Å / Mean I/σ(I) obs: 1.27 / Num. unique obs: 2417 / CC1/2: 0.821

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: De novo Designed Model

Resolution: 1.65→48.61 Å / SU ML: 0.2046 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.069
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.215 1309 5.17 %
Rwork0.1861 24006 -
obs0.1876 25315 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.04 Å2
Refinement stepCycle: LAST / Resolution: 1.65→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 0 96 1962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091919
X-RAY DIFFRACTIONf_angle_d0.96592586
X-RAY DIFFRACTIONf_chiral_restr0.0512307
X-RAY DIFFRACTIONf_plane_restr0.0063331
X-RAY DIFFRACTIONf_dihedral_angle_d20.68611228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.710.3231300.29252565X-RAY DIFFRACTION96.73
1.71-1.790.31041510.26432598X-RAY DIFFRACTION98.92
1.79-1.890.29271260.23532640X-RAY DIFFRACTION99.18
1.89-20.24211500.21432646X-RAY DIFFRACTION99.29
2-2.160.19331500.18612656X-RAY DIFFRACTION99.43
2.16-2.380.21791450.17712670X-RAY DIFFRACTION99.75
2.38-2.720.23321440.17832681X-RAY DIFFRACTION99.86
2.72-3.430.20621610.18752738X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 1.20700788503 Å / Origin y: -11.7881850341 Å / Origin z: 6.09969566996 Å
111213212223313233
T0.213181494222 Å20.0155785162321 Å2-0.0220312759095 Å2-0.204316473239 Å2-0.0189409564753 Å2--0.153395961828 Å2
L1.71839776833 °20.455069963608 °20.0857030677986 °2-1.41101117217 °2-0.073791460588 °2--0.279279051399 °2
S0.0114627355855 Å °0.0344007257472 Å °-0.0349822306762 Å °0.046597506906 Å °-0.0456228499592 Å °0.0778549581528 Å °-0.016592212191 Å °-0.0336834816772 Å °0.0237538462162 Å °
Refinement TLS groupSelection details: all

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