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- PDB-4qks: Crystal Structure of 6xTrp/PV2: de novo designed beta-trefoil arc... -

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Basic information

Entry
Database: PDB / ID: 4qks
TitleCrystal Structure of 6xTrp/PV2: de novo designed beta-trefoil architecture with symmetric primary structure (L22W/L44W/L64W/L85W/L108W/L132W his Primitive Version 2)
ComponentsDE NOVO PROTEIN 6XTRP/PV2
KeywordsDE NOVO PROTEIN / simplified protein design / prebiotic protein / beta-trefoil
Function / homologyTrefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Function and homology information
Biological speciesSynthetic (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLongo, L.M. / Tenorio, C.A. / Blaber, M.
CitationJournal: Protein Sci. / Year: 2015
Title: A single aromatic core mutation converts a designed "primitive" protein from halophile to mesophile folding.
Authors: Longo, L.M. / Tenorio, C.A. / Kumru, O.S. / Middaugh, C.R. / Blaber, M.
History
DepositionJun 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: DE NOVO PROTEIN 6XTRP/PV2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9793
Polymers14,7611
Non-polymers2182
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.138, 48.471, 69.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DE NOVO PROTEIN 6XTRP/PV2 /


Mass: 14760.864 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic (others)
Description: Synthetic sequence derived from human acidic fibroblast growth factor with symmetric deconstruction method and enriched for pre-biotic amino acids.
Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4 M (NH4)2SO4, 0.1 M Tris, 0.07 M Li2SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 17, 2013 / Details: OSMIC CONFOCAL MIRROS
RadiationMonochromator: MULTI-LAYER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 17987 / % possible obs: 98.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 25.79 Å2 / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.045 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.8912 / SU ML: 0.24 / σ(F): 2.01 / Phase error: 17.56 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 852 4.92 %Random
Rwork0.1953 ---
obs0.1971 17307 95.33 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 61.29 Å2 / Biso mean: 26.7528 Å2 / Biso min: 16.13 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 13 136 1124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071041
X-RAY DIFFRACTIONf_angle_d1.0351425
X-RAY DIFFRACTIONf_chiral_restr0.063148
X-RAY DIFFRACTIONf_plane_restr0.004195
X-RAY DIFFRACTIONf_dihedral_angle_d14.607403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.80660.37221230.31712446256987
1.8066-1.94610.2271460.18532683282995
1.9461-2.1420.22091420.1642775291798
2.142-2.45190.21061470.17432829297699
2.4519-3.08890.2441430.19322866300999
3.0889-39.05540.22531510.20262856300795

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