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- PDB-4lpw: Crystal structure of TENCON variant A6 -

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Basic information

Entry
Database: PDB / ID: 4lpw
TitleCrystal structure of TENCON variant A6
ComponentsTENCON variant A6
KeywordsDE NOVO PROTEIN / fibronectin type III fold / alternate scaffold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2014
Title: C-terminal beta-strand swapping in a consensus-derived fibronectin Type III scaffold.
Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Luo, J. / Jacobs, S.A. / Chan, W. / Domingo, D. / Baker, A. / O'Neil, K.T. / Gilliland, G.L.
History
DepositionJul 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: TENCON variant A6
B: TENCON variant A6


Theoretical massNumber of molelcules
Total (without water)22,2472
Polymers22,2472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-27 kcal/mol
Surface area10260 Å2
MethodPISA
2
A: TENCON variant A6
B: TENCON variant A6

A: TENCON variant A6
B: TENCON variant A6

A: TENCON variant A6
B: TENCON variant A6


Theoretical massNumber of molelcules
Total (without water)66,7406
Polymers66,7406
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16300 Å2
ΔGint-103 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.330, 99.330, 99.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein TENCON variant A6


Mass: 11123.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)

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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: 3.67 Å3/Da / Density % sol: 66.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium acetate, pH 5.5, 26% PEG3350, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 1, 2010 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 8281 / Num. obs: 8281 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.45 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TES

3tes


Resolution: 2.8→28.7 Å / σ(F): 1.35 / Phase error: 29.88 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 835 10 %RANDOM
Rwork0.1819 ---
obs0.186 8281 99.9 %-
all-8281 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 0 0 1387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081421
X-RAY DIFFRACTIONf_angle_d1.2061948
X-RAY DIFFRACTIONf_dihedral_angle_d14.339492
X-RAY DIFFRACTIONf_chiral_restr0.081227
X-RAY DIFFRACTIONf_plane_restr0.007253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.9770.28211350.24921220X-RAY DIFFRACTION90
2.977-3.20650.24751350.21341237X-RAY DIFFRACTION90
3.2065-3.52850.25971310.18771226X-RAY DIFFRACTION90
3.5285-4.03750.22511410.19431213X-RAY DIFFRACTION90
4.0375-5.0810.20171430.1491241X-RAY DIFFRACTION90
5.081-26.54820.2021500.16911298X-RAY DIFFRACTION90

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