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- PDB-3ol0: Crystal structure of Monofoil-4P homo-trimer: de novo designed mo... -

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Entry
Database: PDB / ID: 3ol0
TitleCrystal structure of Monofoil-4P homo-trimer: de novo designed monomer trefoil-fold sub-domain which forms homo-trimer assembly
Componentsde novo designed monomer trefoil-fold sub-domain which forms homo-trimer assembly
KeywordsDE NOVO PROTEIN / beta-trefoil / trefoil-fold / synthetic protein / Function-competent only
Function / homologySH3 type barrels. - #30 / SH3 type barrels. / Other non-globular / Special
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.483 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 25, 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

Downloads & links

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Assembly

Deposited unit
A: de novo designed monomer trefoil-fold sub-domain which forms homo-trimer assembly
B: de novo designed monomer trefoil-fold sub-domain which forms homo-trimer assembly
C: de novo designed monomer trefoil-fold sub-domain which forms homo-trimer assembly
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8128
Polymers16,3323
Non-polymers4805
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-70 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.520, 53.478, 65.868
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/peptide de novo designed monomer trefoil-fold sub-domain which forms homo-trimer assembly


Mass: 5443.896 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 monomer 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 monomer 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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2M AMMONIUM SULFATE, 0.1M NA CITRATE, 15MG/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: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 29633 / Num. obs: 29337 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 19.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 82.4
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 16.6 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 8.38 / Num. unique all: 1434 / % possible all: 98.8

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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: 1.483→41.517 Å / SU ML: 0.14 / σ(F): 4.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1385 4.99 %RANDOM
Rwork0.1805 ---
obs0.1817 27734 93.44 %-
all-29633 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.175 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3129 Å20 Å20 Å2
2---3.3053 Å2-0 Å2
3----0.0076 Å2
Refinement stepCycle: LAST / Resolution: 1.483→41.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 25 203 1214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061130
X-RAY DIFFRACTIONf_angle_d1.0691558
X-RAY DIFFRACTIONf_dihedral_angle_d14.01450
X-RAY DIFFRACTIONf_chiral_restr0.072169
X-RAY DIFFRACTIONf_plane_restr0.005208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.483-1.53570.2381150.18252129212977
1.5357-1.59710.22241210.17842389238987
1.5971-1.66980.23511270.17932479247989
1.6698-1.75790.21321380.17232582258293
1.7579-1.8680.18371510.16562668266896
1.868-2.01220.19621370.17822754275498
2.0122-2.21470.21461450.1752795279599
2.2147-2.53520.19081490.17672810281099
2.5352-3.19390.21151440.191328572857100
3.1939-41.53350.19851580.18252886288696

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