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- PDB-4lpu: Crystal structure of TENCON variant P40AR2-32R2 -

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Basic information

Entry
Database: PDB / ID: 4lpu
TitleCrystal structure of TENCON variant P40AR2-32R2
ComponentsTENCON variant P40AR2-32R2
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: 3.4 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 P40AR2-32R2
B: TENCON variant P40AR2-32R2


Theoretical massNumber of molelcules
Total (without water)21,9762
Polymers21,9762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-27 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.730, 84.730, 127.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein TENCON variant P40AR2-32R2


Mass: 10988.093 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 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 25% PEG3000, 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: Dec 17, 2009 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. all: 3822 / Num. obs: 3822 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.4 % / Biso Wilson estimate: 66.5 Å2 / Rmerge(I) obs: 0.101
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 12 % / Rmerge(I) obs: 0.475 / % possible all: 65.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TES

3tes


Resolution: 3.4→15 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.834 / SU B: 40.959 / SU ML: 0.643 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.719 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.33517 167 4.4 %RANDOM
Rwork0.27748 ---
all0.27997 3603 --
obs0.27997 3603 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.37 Å22.68 Å20 Å2
2--5.37 Å20 Å2
3----8.05 Å2
Refinement stepCycle: LAST / Resolution: 3.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 0 0 1390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221426
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9761960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7465184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98324.6354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.4715194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.585154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2226
X-RAY DIFFRACTIONr_gen_planes_refined00.0221098
X-RAY DIFFRACTIONr_mcbond_it0.9052928
X-RAY DIFFRACTIONr_mcangle_it1.75341490
X-RAY DIFFRACTIONr_scbond_it42.87888498
X-RAY DIFFRACTIONr_scangle_it57.10288470
LS refinement shellResolution: 3.4→3.484 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 9 -
Rwork0.339 164 -
obs--65.3 %

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