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- PDB-3snv: Crystal structure of Symfoil-4T Permutation #1: de novo designed ... -

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Basic information

Entry
Database: PDB / ID: 3snv
TitleCrystal structure of Symfoil-4T Permutation #1: de novo designed beta-trefoil architecture with symmetric primary structure
ComponentsSymfoil-4T/Permutation #1 synthetic protein
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBlaber, M. / Longo, L. / Lee, J.
CitationJournal: To be Published
Title: Folding pathway redundancy in symmetric protein architecture
Authors: Longo, L. / Lee, J. / Blaber, M.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Symfoil-4T/Permutation #1 synthetic protein
B: Symfoil-4T/Permutation #1 synthetic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,00212
Polymers31,9892
Non-polymers1,01310
Water1,29772
1
A: Symfoil-4T/Permutation #1 synthetic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5016
Polymers15,9941
Non-polymers5065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Symfoil-4T/Permutation #1 synthetic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5016
Polymers15,9941
Non-polymers5065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.667, 56.667, 81.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Symfoil-4T/Permutation #1 synthetic protein


Mass: 15994.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS A CIRCULAR PERMUTATION OF THE SYMFOIL-4T PROTEIN (PDB ACCESSION 3O4B). IN THIS PERMUTATION ...THIS IS A CIRCULAR PERMUTATION OF THE SYMFOIL-4T PROTEIN (PDB ACCESSION 3O4B). IN THIS PERMUTATION THE NEW N-TERMINAL IS RESIDUE NUMBER THR19 (AFTER AN N-TERMINAL HIS-TAGGED LEADER SEQUENCE).

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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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.9 M ammonium sulfate, 0.2 M lithium sulfate, 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 RUH2R / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 19, 2010 / Details: Osmic confocal
RadiationMonochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 13099 / Num. obs: 12051 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.64 / Num. unique all: 636 / % possible all: 57.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O4B

3o4b


Resolution: 2.2→23.226 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7957 / SU ML: 0.39 / σ(F): 2 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 585 4.9 %RANDOM
Rwork0.1988 ---
obs0.2017 11928 91.28 %-
all-13099 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.747 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 95.08 Å2 / Biso mean: 40.2462 Å2 / Biso min: 15.04 Å2
Baniso -1Baniso -2Baniso -3
1--4.9857 Å2-0 Å20 Å2
2---4.9857 Å2-0 Å2
3---9.9714 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 56 72 2061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032007
X-RAY DIFFRACTIONf_angle_d0.5712722
X-RAY DIFFRACTIONf_chiral_restr0.041295
X-RAY DIFFRACTIONf_plane_restr0.002366
X-RAY DIFFRACTIONf_dihedral_angle_d14.833754
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 (%)
2.2-2.42150.31321070.25982153226069
2.4215-2.77140.34971590.24112968312796
2.7714-3.48970.27711580.214230973255100
3.4897-23.2270.21091610.167431253286100

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