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

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Basic information

Entry
Database: PDB / ID: 1sne
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
Function / homologyISOPROPYL ALCOHOL
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 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 / chem_comp_atom ...atom_site / 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 / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2803
Polymers5,2202
Non-polymers601
Water1,24369
1
A: tetrameric beta-beta-alpha mini-protein
B: tetrameric beta-beta-alpha mini-protein
hetero molecules

A: tetrameric beta-beta-alpha mini-protein
B: tetrameric beta-beta-alpha mini-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5606
Polymers10,4394
Non-polymers1202
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Unit cell
Length a, b, c (Å)57.912, 21.325, 31.896
Angle α, β, γ (deg.)90.00, 121.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-87-

HOH

21A-89-

HOH

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Components

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


Mass: 2609.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The protein was chemically synthesized.
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.61 Å3/Da / Density % sol: 23.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES-Na, 10% v/v i-propanol, 20% w/v PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.978031, 0.97902, 0.949320
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9780311
20.979021
30.949321
ReflectionResolution: 1.5→99 Å / Num. all: 7811 / Num. obs: 7811 / % possible obs: 74.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 33.6
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 7.1 / Num. unique all: 169 / % possible all: 16.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→27.25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1233606.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.183 786 10.1 %RANDOM
Rwork0.169 ---
all0.169 7769 --
obs0.169 7769 74.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.1948 Å2 / ksol: 0.327503 e/Å3
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-0.16 Å2
2--2.18 Å20 Å2
3----1.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms393 0 0 73 466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 29 7.6 %
Rwork0.208 351 -
obs--21.4 %

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