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- PDB-3teu: Crystal structure of fibcon -

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Basic information

Entry
Database: PDB / ID: 3teu
TitleCrystal structure of fibcon
ComponentsFibcon
KeywordsDE NOVO PROTEIN / FN3 domain / fibronectin tpye III domain / consensus design / stability
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 1,4-DIETHYLENE DIOXIDE
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.002 Å
AuthorsLuo, J. / Jacobs, S. / Teplyakov, A. / Obmolova, G. / O'Neil, K. / Gilliland, G.
CitationJournal: Protein Eng.Des.Sel. / Year: 2012
Title: Design of novel FN3 domains with high stability by a consensus sequence approach.
Authors: Jacobs, S.A. / Diem, M.D. / Luo, J. / Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. / O'Neil, K.T.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Fibcon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4892
Polymers10,4001
Non-polymers881
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.390, 40.070, 61.520
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 Fibcon


Mass: 10400.417 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.68 Å3/Da / Density % sol: 26.9 %
Crystal growTemperature: 297 K / pH: 4.5
Details: 0.1 M sodium acetate, 23% PEG8000, 5% PEG 400, 3% dioxane, pH 4.5, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 17, 2010
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 37699 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 1→1.02 Å / % possible all: 90.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: starting model 1FNF

1fnf


Resolution: 1.002→33.576 Å / SU ML: 0.08 / σ(F): 2.04 / Phase error: 9.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1389 1879 4.99 %
Rwork0.1105 --
obs0.1119 37662 97.88 %
all-37663 -
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.003 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6041 Å2-0 Å20 Å2
2---0.087 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.002→33.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms733 0 6 137 876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.028863
X-RAY DIFFRACTIONf_angle_d2.5311207
X-RAY DIFFRACTIONf_dihedral_angle_d15.411309
X-RAY DIFFRACTIONf_chiral_restr0.144149
X-RAY DIFFRACTIONf_plane_restr0.014159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0022-1.02930.16061350.12172494X-RAY DIFFRACTION90
1.0293-1.05960.13891330.10532664X-RAY DIFFRACTION96
1.0596-1.09380.12721380.09472703X-RAY DIFFRACTION96
1.0938-1.13290.12321230.07942682X-RAY DIFFRACTION97
1.1329-1.17820.10151420.07212694X-RAY DIFFRACTION97
1.1782-1.23180.0981300.07582772X-RAY DIFFRACTION99
1.2318-1.29680.10211490.07622739X-RAY DIFFRACTION99
1.2968-1.3780.10771440.08122780X-RAY DIFFRACTION100
1.378-1.48440.10791620.08712804X-RAY DIFFRACTION100
1.4844-1.63380.10961630.09332784X-RAY DIFFRACTION100
1.6338-1.87020.12911450.09912826X-RAY DIFFRACTION100
1.8702-2.35620.13511540.10242867X-RAY DIFFRACTION100
2.3562-33.59480.18491610.15492974X-RAY DIFFRACTION99

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