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- PDB-3q7w: Crystal structure of Symfoil-4P/PV1: de novo designed beta-trefoi... -

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Basic information

Entry
Database: PDB / ID: 3q7w
TitleCrystal structure of Symfoil-4P/PV1: de novo designed beta-trefoil architecture with symmetric primary structure, primitive version 1
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBlaber, M. / Lee, J.
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 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Feb 20, 2013Group: Database references
Revision 1.4Feb 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)14,7193
Polymers14,5271
Non-polymers1922
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.467, 46.643, 63.921
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 designed beta-trefoil architecture with symmetric primary structure


Mass: 14526.649 Da / Num. of mol.: 1 / Source method: obtained synthetically
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.
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.5M ammonium sulfate, 0.1M HEPES, 0.1M Lithium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 18903 / Num. obs: 17284 / % possible obs: 91.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Biso Wilson estimate: 12.04 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 43.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 6.2 / Num. unique all: 921 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→26.917 Å / SU ML: 0.17 / σ(F): 4.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 852 4.93 %RANDOM
Rwork0.1669 ---
obs0.169 17284 91.05 %-
all-18903 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.305 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1265 Å20 Å2-0 Å2
2--0.0772 Å20 Å2
3----2.2036 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 10 154 1121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061041
X-RAY DIFFRACTIONf_angle_d1.0771424
X-RAY DIFFRACTIONf_dihedral_angle_d14.77420
X-RAY DIFFRACTIONf_chiral_restr0.074154
X-RAY DIFFRACTIONf_plane_restr0.005201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.5-1.59550.19381060.17692215221575
1.5955-1.71860.23041330.16582537253786
1.7186-1.89150.18291440.16152734273492
1.8915-2.16520.22791540.1582882288297
2.1652-2.72750.20821530.17042977297798
2.7275-26.92140.2131620.16873087308798

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