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- PDB-4lpx: Crystal structure of TENCON variant D4 -

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Basic information

Entry
Database: PDB / ID: 4lpx
TitleCrystal structure of TENCON variant D4
ComponentsTENCON variant D4
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: 1.9 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 D4


Theoretical massNumber of molelcules
Total (without water)10,9871
Polymers10,9871
Non-polymers00
Water1,63991
1
A: TENCON variant D4

A: TENCON variant D4


Theoretical massNumber of molelcules
Total (without water)21,9742
Polymers21,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_454y-1/4,x+1/4,-z-3/41
Buried area4220 Å2
ΔGint-29 kcal/mol
Surface area11070 Å2
MethodPISA
2
A: TENCON variant D4
x 6


Theoretical massNumber of molelcules
Total (without water)65,9236
Polymers65,9236
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
crystal symmetry operation13_454y-1/4,x+1/4,-z-3/41
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
Buried area17680 Å2
ΔGint-131 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.630, 100.630, 100.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein TENCON variant D4


Mass: 10987.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.86 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 1.5 M ammonium sulfate, 5% PEG400, 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: Mar 17, 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: 1.9→30 Å / Num. all: 16040 / Num. obs: 16040 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25.3 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.176 / % possible all: 90.2

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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: 1.9→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.731 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.116 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24167 667 4.8 %RANDOM
Rwork0.20763 ---
all0.20929 13183 --
obs0.20929 13183 96.3 %-
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: 34.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 0 91 818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022744
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9881020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.484596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13425.51729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.08415109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.578152
X-RAY DIFFRACTIONr_chiral_restr0.0930.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022568
X-RAY DIFFRACTIONr_mcbond_it3.6312485
X-RAY DIFFRACTIONr_mcangle_it5.8094785
X-RAY DIFFRACTIONr_scbond_it28.01288259
X-RAY DIFFRACTIONr_scangle_it25.65288235
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 47 -
Rwork0.259 896 -
obs--90.2 %

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