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- PDB-3ogf: Crystal structure of Difoil-4P homo-trimer: de novo designed dime... -

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Basic information

Entry
Database: PDB / ID: 3ogf
TitleCrystal structure of Difoil-4P homo-trimer: de novo designed dimeric trefoil-fold sub-domain which forms homo-trimer assembly
Componentsde novo designed dimeric trefoil-fold sub-domain which forms homo-trimer assembly
KeywordsDE NOVO PROTEIN / beta-trefoil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.864 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
DepositionAug 16, 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 dimeric trefoil-fold sub-domain which forms homo-trimer assembly
B: de novo designed dimeric trefoil-fold sub-domain which forms homo-trimer assembly
C: de novo designed dimeric trefoil-fold sub-domain which forms homo-trimer assembly
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5076
Polymers30,2193
Non-polymers2883
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-53 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.242, 85.414, 86.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein de novo designed dimeric trefoil-fold sub-domain which forms homo-trimer assembly


Mass: 10072.896 Da / Num. of mol.: 3
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 forms a dimeric trefoil-fold sub-domain ...Details: Synthetic sequence derived from human acidic fibroblast growth factor with a symmetric deconstruction method. The protein produced by this sequence forms a dimeric trefoil-fold sub-domain and exists as a homo-trimer assembly adopting a beta-trefoil architecture.
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2M ammonium sulfate, 0.1M sodium citrate, 17mg/mL protein concentration, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 6757 / Num. obs: 6415 / % possible obs: 94.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Biso Wilson estimate: 62.68 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 33
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.3 / Num. unique all: 218 / % possible all: 61.8

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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: 2.864→43.043 Å / SU ML: 2.37 / σ(F): 0.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3111 315 4.91 %RANDOM
Rwork0.2269 ---
obs0.2308 6415 89.35 %-
all-6757 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.182 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--29.4168 Å20 Å20 Å2
2--12.9741 Å2-0 Å2
3---16.4426 Å2
Refinement stepCycle: LAST / Resolution: 2.864→43.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 15 0 1917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021965
X-RAY DIFFRACTIONf_angle_d0.5492672
X-RAY DIFFRACTIONf_dihedral_angle_d13.228754
X-RAY DIFFRACTIONf_chiral_restr0.034292
X-RAY DIFFRACTIONf_plane_restr0.003366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.864-2.90.35651450.20572676267680
3.6086-43.04780.29541700.23343424342498

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