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- PDB-3o4a: Crystal structure of Symfoil-2: de novo designed beta-trefoil arc... -

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Basic information

Entry
Database: PDB / ID: 3o4a
TitleCrystal structure of Symfoil-2: 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
B: de novo designed beta-trefoil architecture with symmetric primary structure
C: de novo designed beta-trefoil architecture with symmetric primary structure
D: de novo designed beta-trefoil architecture with symmetric primary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,59018
Polymers63,1414
Non-polymers1,44914
Water11,241624
1
A: de novo designed beta-trefoil architecture with symmetric primary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0994
Polymers15,7851
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: de novo designed beta-trefoil architecture with symmetric primary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1955
Polymers15,7851
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: de novo designed beta-trefoil architecture with symmetric primary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1955
Polymers15,7851
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: de novo designed beta-trefoil architecture with symmetric primary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0994
Polymers15,7851
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.701, 53.641, 85.336
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15785.144 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 1.84 Å3/Da / Density % sol: 33.07 %
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: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2009
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 79285 / Num. obs: 73170 / % possible obs: 92.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 14.72 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 34.1
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3797 / % possible all: 95.1

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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→45.414 Å / SU ML: 1.21 / σ(F): 0.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 1828 2.5 %RANDOM
Rwork0.1861 ---
obs0.1868 73170 90.03 %-
all-79285 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.653 Å2 / ksol: 0.407 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6536 Å2-0 Å20.0115 Å2
2---2.0831 Å20 Å2
3----1.5705 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 82 624 4538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064408
X-RAY DIFFRACTIONf_angle_d1.096042
X-RAY DIFFRACTIONf_dihedral_angle_d181756
X-RAY DIFFRACTIONf_chiral_restr0.075645
X-RAY DIFFRACTIONf_plane_restr0.005826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.45-1.50210.30031570.2586221622179
1.5021-1.56220.26171700.22696619661984
1.5622-1.63330.26111700.2136592659283
1.6333-1.71950.24511770.2046611661184
1.7195-1.82720.21351700.19026985698588
1.8272-1.96830.22861790.18127226722692
1.9683-2.16630.24582020.17377645764596
2.1663-2.47980.20211990.18217685768597
2.4798-3.12420.21232020.17957833783398
3.1242-45.43640.18492020.1737925792598

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