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- PDB-4k5c: From DARPins to LoopDARPins: Novel LoopDARPin Design Allows the S... -

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Basic information

Entry
Database: PDB / ID: 4k5c
TitleFrom DARPins to LoopDARPins: Novel LoopDARPin Design Allows the Selection of Low Picomolar Binders in a Single Round of Ribosome Display
ComponentsLoop Designed Ankyrin Repeat Protein Nran1_G06_C
KeywordsSTRUCTURAL PROTEIN
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSchilling, J. / Schoeppe, J. / Plueckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: From DARPins to LoopDARPins: novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display
Authors: Schilling, J. / Schoeppe, J. / Plueckthun, A.
History
DepositionApr 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Loop Designed Ankyrin Repeat Protein Nran1_G06_C
B: Loop Designed Ankyrin Repeat Protein Nran1_G06_C


Theoretical massNumber of molelcules
Total (without water)39,6222
Polymers39,6222
Non-polymers00
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-17 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.600, 63.900, 113.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Loop Designed Ankyrin Repeat Protein Nran1_G06_C


Mass: 19811.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL1-blue / Plasmid: pQIq / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Na-cacodylate, 0.2M Li2SO4, 8% PEG20000, 8% PEG550 MME, pH 6.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 40279 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.707 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.740.7670.4672.519285295729420.56399.5
1.74-1.790.5490.3693.189125286628540.44499.6
1.79-1.840.4250.2944.29630282928210.3599.7
1.84-1.90.3560.2475.019206270627000.29499.8
1.9-1.960.2560.1836.468831262926250.21799.8
1.96-2.030.2060.1477.688395255625380.17599.3
2.03-2.110.1520.1069.877731248124610.12899.2
2.11-2.190.1220.09511.257860238723750.11399.5
2.19-2.290.1010.08213.327771228522760.09899.6
2.29-2.40.0840.0715.267439220221920.08499.5
2.4-2.530.0650.0617.496952209220770.07199.3
2.53-2.690.0570.04919.496165198319540.05998.5
2.69-2.870.0490.04522.246157187218650.05399.6
2.87-3.10.0370.03726.315944175317450.04499.5
3.1-3.40.0310.03428.175309160215970.04199.7
3.4-3.80.0280.03431.294642148214500.0497.8
3.8-4.390.0240.02932.954015130412930.03599.2
4.39-5.380.0230.02934.733719113111260.03599.6
5.38-7.60.0280.0330.1525988818700.03698.8
7.60.0240.0332.8315455325180.03697.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.46 Å
Translation2.5 Å45.46 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.456 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8786 / SU ML: 0.4 / σ(F): 1.99 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1969 2016 5.01 %
Rwork0.1713 --
obs0.1726 40275 99.37 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.934 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 75.72 Å2 / Biso mean: 21.5691 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.6248 Å20 Å2-0 Å2
2--4.0046 Å20 Å2
3----3.3798 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 0 488 3079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062693
X-RAY DIFFRACTIONf_angle_d0.9913673
X-RAY DIFFRACTIONf_chiral_restr0.064416
X-RAY DIFFRACTIONf_plane_restr0.005487
X-RAY DIFFRACTIONf_dihedral_angle_d12.97950
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.27921380.25742695283399
1.7425-1.78960.28051550.240826712826100
1.7896-1.84230.26261400.222327382878100
1.8423-1.90180.24141600.207926682828100
1.9018-1.96970.28431360.184227312867100
1.9697-2.04860.18941530.1782664281799
2.0486-2.14180.2111270.16122735286299
2.1418-2.25470.20621430.17327182861100
2.2547-2.3960.19421380.167227172855100
2.396-2.5810.20141380.16782736287499
2.581-2.84070.21491390.15922732287199
2.8407-3.25160.17241390.165827812920100
3.2516-4.09630.14181520.1482757290999
4.0963-45.47230.19351580.16662916307499

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