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- PDB-3p6j: Crystal structure of Symfoil-4T Permutation #3: de novo designed ... -

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Basic information

Entry
Database: PDB / ID: 3p6j
TitleCrystal structure of Symfoil-4T Permutation #3: 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: 1.35 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)15,8771
Polymers15,8771
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.860, 57.698, 61.412
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 de novo designed beta-trefoil architecture with symmetric primary structure


Mass: 15877.192 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.0M sodium citrate, 0.1M sodium cacodylate, 10mg/mL protein concentration, pH 6.5, 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: 1.35→50 Å / Num. all: 36190 / Num. obs: 33256 / % possible obs: 91.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 12 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 61.7
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1739 / % possible all: 94.1

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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: 1.35→36.375 Å / SU ML: 0.12 / σ(F): 4.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1661 1647 4.95 %RANDOM
Rwork0.1463 ---
obs0.1473 33256 89.19 %-
all-36190 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.109 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0867 Å20 Å2-0 Å2
2---1.1734 Å20 Å2
3---1.2601 Å2
Refinement stepCycle: LAST / Resolution: 1.35→36.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 0 181 1147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061111
X-RAY DIFFRACTIONf_angle_d1.1091538
X-RAY DIFFRACTIONf_dihedral_angle_d13.684465
X-RAY DIFFRACTIONf_chiral_restr0.072173
X-RAY DIFFRACTIONf_plane_restr0.006215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.35-1.39820.16171190.1409X-RAY DIFFRACTION243769
1.3982-1.45420.16671470.1237X-RAY DIFFRACTION267377
1.4542-1.52040.15481520.1101X-RAY DIFFRACTION289082
1.5204-1.60050.13371590.0997X-RAY DIFFRACTION306188
1.6005-1.70080.12971650.1052X-RAY DIFFRACTION315190
1.7008-1.83210.1271710.12X-RAY DIFFRACTION330194
1.8321-2.01650.14361810.1339X-RAY DIFFRACTION340196
2.0165-2.30830.17511810.146X-RAY DIFFRACTION348098
2.3083-2.9080.17411800.1657X-RAY DIFFRACTION354399
2.908-36.38790.18771920.1664X-RAY DIFFRACTION367298

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