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- PDB-1mj0: SANK E3_5: an artificial Ankyrin repeat protein -

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Basic information

Entry
Database: PDB / ID: 1mj0
TitleSANK E3_5: an artificial Ankyrin repeat protein
ComponentsSANK E3_5 Protein
KeywordsDE NOVO PROTEIN / Ankyrin repeat / protein engineering / consensus
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / :
Function and homology information
Biological speciesDesigned synthetic gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.031 Å
AuthorsKohl, A. / Binz, H.K. / Forrer, P. / Stumpp, M.T. / Plueckthun, A. / Gruetter, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Designed to be stable: Crystal structure of a consensus ankyrin repeat protein
Authors: Kohl, A. / Binz, H.K. / Forrer, P. / Stumpp, M.T. / Plueckthun, A. / Gruetter, M.G.
History
DepositionAug 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SANK E3_5 Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0534
Polymers17,7391
Non-polymers3143
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.864, 47.360, 47.003
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-323-

HOH

21A-324-

HOH

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Components

#1: Protein SANK E3_5 Protein


Mass: 17738.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Designed synthetic gene (others) / Plasmid: pQE30 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: GenBank: 28274847
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 4000, Li2SO4, NH4OAc, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1droppH8.0
2150 mM1dropNaCl
39 mg/mlprotein1drop
416-22 %PEG40001reservoir
50.2 M1reservoirLi2SO4
60.1 M1reservoirpH4.6-5.0NH4OAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 2001
RadiationMonochromator: Mirror, Biophysics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→20 Å / Num. all: 11291 / Num. obs: 11091 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.4 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.1 / Net I/σ(I): 20.3
Reflection shellResolution: 2.02→2.09 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 48.8 / Num. unique all: 917 / Rsym value: 0.33 / % possible all: 83.8
Reflection
*PLUS
Highest resolution: 2.03 Å / Num. obs: 11291 / % possible obs: 98.4 % / Num. measured all: 173985 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 83.8 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AWC

1awc


Resolution: 2.031→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.445 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.209 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22971 1140 10.3 %RANDOM
Rwork0.17917 ---
obs0.18432 9924 99.45 %-
all-11091 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.984 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.031→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 18 178 1390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211200
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9691639
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0973162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95915189
X-RAY DIFFRACTIONr_chiral_restr0.1310.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02906
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.3668
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.5121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.343
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2431.5783
X-RAY DIFFRACTIONr_mcangle_it2.04721245
X-RAY DIFFRACTIONr_scbond_it3.5653417
X-RAY DIFFRACTIONr_scangle_it5.3724.5394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.031→2.083 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 54
Rwork0.197 685
Refinement
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.926

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