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- PDB-1sn9: An Oligomeric Domain-Swapped Beta-Beta-Alpha Mini-Protein -

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Basic information

Entry
Database: PDB / ID: 1sn9
TitleAn Oligomeric Domain-Swapped Beta-Beta-Alpha Mini-Protein
Componentstetrameric beta-beta-alpha mini-protein
KeywordsDE NOVO PROTEIN / protein design / domain swapping / mini-protein / oligomerization
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsAli, M.H. / Peisach, E. / Allen, K.N. / Imperiali, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: X-ray structure analysis of a designed oligomeric miniprotein reveals a discrete quaternary architecture
Authors: Ali, M.H. / Peisach, E. / Allen, K.N. / Imperiali, B.
History
DepositionMar 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.0May 8, 2024Group: Atomic model / Category: atom_site / atom_site_anisotrop
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tetrameric beta-beta-alpha mini-protein
B: tetrameric beta-beta-alpha mini-protein
C: tetrameric beta-beta-alpha mini-protein
D: tetrameric beta-beta-alpha mini-protein


Theoretical massNumber of molelcules
Total (without water)10,1764
Polymers10,1764
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.939, 56.172, 32.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-141-

HOH

21A-147-

HOH

31B-70-

HOH

41D-88-

HOH

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Components

#1: Protein/peptide
tetrameric beta-beta-alpha mini-protein / BBAT


Mass: 2543.876 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The protein was chemically synthesized.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.74 Å3/Da / Density % sol: 29.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% t-butanol, 0.1M TRIS buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→99 Å / Num. obs: 21067 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 26.8
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.7 / Num. unique all: 610 / % possible all: 54.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: refined structure of Gln18SeMet selenomethionine derivative of BBAT

Resolution: 1.2→99 Å / Num. parameters: 8097 / Num. restraintsaints: 10728 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2854 1983 10.1 %RANDOM
Rwork0.1881 ---
obs0.1903 19671 86.5 %-
all-19671 --
Displacement parametersBiso mean: 22.3 Å2
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 843.5
Refinement stepCycle: LAST / Resolution: 1.2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 0 118 931
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.032
X-RAY DIFFRACTIONs_angle_d0.039
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0234
X-RAY DIFFRACTIONs_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.109
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0.084

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