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- PDB-3o49: Crystal structure of Symfoil-1: de novo designed beta-trefoil arc... -

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Basic information

Entry
Database: PDB / ID: 3o49
TitleCrystal structure of Symfoil-1: 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: 1.45 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)15,9613
Polymers15,7431
Non-polymers2182
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.365, 53.351, 85.175
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: 15743.063 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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.82 Å3/Da / Density % sol: 32.31 %
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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2009
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 20483 / Num. obs: 19854 / % possible obs: 96.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7 % / Biso Wilson estimate: 18.86 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 53.6
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.6 / Num. unique all: 868 / % possible all: 85.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→45.214 Å / SU ML: 1.15 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1937 9.76 %RANDOM
Rwork0.1958 ---
obs0.1989 19854 95.45 %-
all-20483 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.978 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6536 Å20 Å2-0 Å2
2--5.4726 Å20 Å2
3----1.819 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 13 152 1120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071031
X-RAY DIFFRACTIONf_angle_d1.1351405
X-RAY DIFFRACTIONf_dihedral_angle_d17.607401
X-RAY DIFFRACTIONf_chiral_restr0.072153
X-RAY DIFFRACTIONf_plane_restr0.005192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.45-1.50060.23871570.25121454145479
1.5006-1.56070.28521720.23411701170191
1.5607-1.63170.28921920.22921729172995
1.6317-1.71780.27032000.22281794179497
1.7178-1.82540.26862010.21871805180598
1.8254-1.96640.25561860.21351853185398
1.9664-2.16420.22722060.19331856185699
2.1642-2.47740.22192020.19211852185299
2.4774-3.12110.24012040.186419091909100
3.1211-45.23570.19272170.17731964196499

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