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- PDB-4d8h: Crystal structure of Symfoil-4P/PV2: de novo designed beta-trefoi... -

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Basic information

Entry
Database: PDB / ID: 4d8h
TitleCrystal structure of Symfoil-4P/PV2: de novo designed beta-trefoil architecture with symmetric primary structure, primitive version 2 (6xLeu / PV1)
Componentsde novo protein
KeywordsDE NOVO PROTEIN / beta-trefoil / symmetric / pre-biotic / Symfoil
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: 1.901 Å
AuthorsBlaber, M. / Longo, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Simplified protein design biased for prebiotic amino acids yields a foldable, halophilic protein.
Authors: Longo, L.M. / Lee, J. / Blaber, M.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Dec 18, 2013Group: Structure summary
Revision 1.4Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5413
Polymers14,3231
Non-polymers2182
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.584, 48.696, 64.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein de novo protein


Mass: 14322.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Synthetic sequence derived from human acidic fibroblast growth factor with symmetric deconstruction method and enriched for pre-biotic amino acids.
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


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


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


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ~15 mg/mL protein concentration, 1.5 M (NH4)2SO4, 0.11 M Li2SO4, 0.1 M Tris, 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 / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2011 / Details: Osmic Confocal Mirrors
RadiationMonochromator: Multi-layer mirrors / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 12143 / Num. obs: 11803 / % possible obs: 97.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.095 / Χ2: 1.913 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.965.80.3427560.753176.2
1.96-2.028.10.2789110.84191.5
2.02-2.0911.50.2489721.015199
2.09-2.1713.30.29911.0931100
2.17-2.2713.60.1739931.2191100
2.27-2.3913.60.14410071.3491100
2.39-2.5413.70.1389841.4651100
2.54-2.7413.60.11810191.757199.9
2.74-3.0113.60.10310112.017199.7
3.01-3.4513.30.08110152.626199.7
3.45-4.34130.06810343.238199.4
4.34-2012.80.05911103.9891100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
DENZOdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→19.99 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8945 / SU ML: 0.43 / σ(F): 2.01 / Phase error: 16.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 579 5.02 %Random 5%
Rwork0.1647 ---
obs0.1671 11533 95.24 %-
all-12143 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.456 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 64.54 Å2 / Biso mean: 20.2147 Å2 / Biso min: 6.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.0261 Å2-0 Å20 Å2
2---1.2013 Å2-0 Å2
3---1.1752 Å2
Refinement stepCycle: LAST / Resolution: 1.901→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 13 177 1129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006998
X-RAY DIFFRACTIONf_angle_d1.0661361
X-RAY DIFFRACTIONf_chiral_restr0.071154
X-RAY DIFFRACTIONf_plane_restr0.006192
X-RAY DIFFRACTIONf_dihedral_angle_d15.639399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9008-2.09190.27111360.20112414255086
2.0919-2.39420.18951400.14132778291898
2.3942-3.01470.22061460.15432819296598
3.0147-19.99090.20611570.17122943310099

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