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- PDB-1xof: Heterooligomeric Beta Beta Alpha Miniprotein -

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Basic information

Entry
Database: PDB / ID: 1xof
TitleHeterooligomeric Beta Beta Alpha Miniprotein
Components(BBAhetT1) x 2
KeywordsDE NOVO PROTEIN / protein design / heterooligomer / heterotetramer
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAli, M.H. / Taylor, C.M. / Grigoryan, G. / Allen, K.N. / Imperiali, B. / Keating, A.E.
CitationJournal: Structure / Year: 2005
Title: Design of a Heterospecific, Tetrameric, 21-Residue Miniprotein with Mixed alpha/beta Structure.
Authors: Ali, M.H. / Taylor, C.M. / Grigoryan, G. / Allen, K.N. / Imperiali, B. / Keating, A.E.
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
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.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: BBAhetT1
B: BBAhetT1


Theoretical massNumber of molelcules
Total (without water)5,1882
Polymers5,1882
Non-polymers00
Water93752
1
A: BBAhetT1
B: BBAhetT1

A: BBAhetT1
B: BBAhetT1


Theoretical massNumber of molelcules
Total (without water)10,3764
Polymers10,3764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Unit cell
Length a, b, c (Å)41.695, 41.695, 51.332
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide BBAhetT1


Mass: 2548.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis
#2: Protein/peptide BBAhetT1


Mass: 2639.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.35 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100 mM Na HEPES buffer pH 7.5, 10% v/v i-propanol, 20% w/v PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→17 Å / Num. all: 3865 / Num. obs: 3865 / Biso Wilson estimate: 27.7 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→17 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1689008.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 380 10.1 %RANDOM
Rwork0.222 ---
all0.222 3865 --
obs0.222 3749 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.0638 Å2 / ksol: 0.290901 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-5.69 Å20 Å2
2--0.36 Å20 Å2
3----0.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.95→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms391 0 0 52 443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.95→2.02 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.325 35 9.5 %
Rwork0.261 332 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DAMINO.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMDAMINO.TOP
X-RAY DIFFRACTION4ION.PARAMPROTEIN_BREAK.TOP

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