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- PDB-3p6i: Crystal structure of Symfoil-4T Permutation #2: de novo designed ... -

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Basic information

Entry
Database: PDB / ID: 3p6i
TitleCrystal structure of Symfoil-4T Permutation #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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsBlaber, M. / Lee, J.
CitationJournal: To be Published
Title: Permutations study of de novo designed symmetric beta-trefoil architecture
Authors: Blaber, M. / Lee, J.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 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)16,0673
Polymers15,8491
Non-polymers2182
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.901, 53.258, 84.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 15849.183 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Circularly permuted synthetic sequence derived from human acidic fibroblast growth factor with a symmetric deconstruction method. The protein produced by this sequence adopts a beta-trefoil ...Details: Circularly permuted 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 31.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2M ammonium sulfate, 0.2M Li2SO4, 0.1M Tris, 17mg/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: 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: 1.32→50 Å / Num. all: 27352 / Num. obs: 25102 / % possible obs: 91.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 35.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 106.5
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1301 / % possible all: 95.7

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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: 1.32→36.797 Å / σ(F): 4.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1781 1257 -RANDOM
Rwork0.1464 ---
obs0.148 25102 91.47 %-
all-27352 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2965 Å20 Å20 Å2
2--1.2914 Å2-0 Å2
Refinement stepCycle: LAST / Resolution: 1.32→36.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 13 151 1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051063
X-RAY DIFFRACTIONf_angle_d0.9661456
X-RAY DIFFRACTIONf_dihedral_angle_d13.213418
X-RAY DIFFRACTIONf_chiral_restr0.059164
X-RAY DIFFRACTIONf_plane_restr0.004197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.32-1.37220.2436900.20291689168959
1.3722-1.43460.22691210.17612386238683
1.4346-1.51020.2461400.15272607260792
1.5102-1.60490.22541460.13832729272995
1.6049-1.72880.21481460.1352777277797
1.7288-1.90270.17991520.12742831283198
1.9027-2.17810.1671490.13512890289099
2.1781-2.7440.16211550.136929122912100
2.744-36.81180.16331580.15633024302499

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