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- PDB-3o4d: Crystal structure of Symfoil-4P: de novo designed beta-trefoil ar... -

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Basic information

Entry
Database: PDB / ID: 3o4d
TitleCrystal structure of Symfoil-4P: de novo designed beta-trefoil architecture with symmetric primary structure
Componentsde novo designed beta-trefoil architecture with symmetric primary structure
KeywordsDE NOVO 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 construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLee, J. / Blaber, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Experimental support for the evolution of symmetric protein architecture from a simple peptide motif.
Authors: Lee, J. / Blaber, M.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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 designed beta-trefoil architecture with symmetric primary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2135
Polymers15,8631
Non-polymers3504
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.372, 53.151, 84.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein de novo designed beta-trefoil architecture with symmetric primary structure


Mass: 15863.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Synthetic sequence derived from human acidic fibroblast growth factor with a symmetric deconstruction method. The protein produced by this sequence adopts a beta-trefoil architecture with ...Details: Synthetic sequence derived from human acidic fibroblast growth factor with a symmetric deconstruction method. The protein produced by this sequence adopts a beta-trefoil architecture with symmetric primary structure.
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.79 Å3/Da / Density % sol: 31.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M ammonium sulfate, 0.2M Li2SO4, 0.1M Tris, 15mg/mL protein concentration, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 13546 / Num. obs: 13224 / % possible obs: 97.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 59.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 7 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 4.5 / Num. unique all: 503 / % possible all: 73.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→42.39 Å / SU ML: 0.23 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 667 5.04 %RANDOM
Rwork0.1895 ---
obs0.1914 13224 93.56 %-
all-13546 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.956 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.2335 Å2-0 Å2-0 Å2
2---5.5988 Å20 Å2
3----2.6347 Å2
Refinement stepCycle: LAST / Resolution: 1.65→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 19 93 1072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071035
X-RAY DIFFRACTIONf_angle_d1.1241415
X-RAY DIFFRACTIONf_dihedral_angle_d15.437405
X-RAY DIFFRACTIONf_chiral_restr0.074154
X-RAY DIFFRACTIONf_plane_restr0.004193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.65-1.77410.32051120.22962031203178
1.7741-1.95260.26061270.2112507250794
1.9526-2.23520.23721360.19122599259997
2.2352-2.8160.24431420.19152650265099
2.816-42.4040.19731500.1782770277099

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