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- PDB-8pf0: Diubiquitin-derived artificial binding protein (Affilin) variant ... -

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Basic information

Entry
Database: PDB / ID: 8pf0
TitleDiubiquitin-derived artificial binding protein (Affilin) variant Af1 specific to oncofetal fibronectin
ComponentsAffilin variant Af1 (77405)
KeywordsDE NOVO PROTEIN / extra domain B / EDB / oncofetal fibronectin / ubiquitin / diubiqutin / Affilin / beta strand register shift / strand slippage / scaffold / artificial binding protein / plasticity / directed evolution
Function / homologyCOPPER (II) ION / IMIDAZOLE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsParthier, C. / Katzschmann, A. / Fiedler, E. / Haupts, U. / Reimann, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Ubiquitin-derived artificial binding proteins targeting oncofetal fibronectin reveal scaffold plasticity by beta-strand slippage
Authors: Katzschmann, A. / Fiedler, E. / Haupts, U. / Reimann, A. / Settele, F. / Gloser-Braeunig, M. / Parthier, C.
History
DepositionJun 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Affilin variant Af1 (77405)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9217
Polymers17,5291
Non-polymers3926
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-23 kcal/mol
Surface area9740 Å2
Unit cell
Length a, b, c (Å)62.767, 62.767, 67.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Affilin variant Af1 (77405)


Mass: 17529.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Cu
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.81 Å3/Da / Density % sol: 67.73 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Imidazol/MES, 60 mM calcium/magnesium chloride, 30% PEG 8000/ethylene glycol (w/v), 10 mM copper(II)chloride dehydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 26176 / % possible obs: 99.5 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.036 / Net I/σ(I): 22.88
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.30.38731890.910.4511
2.3-2.40.33527170.9170.3891
2.4-2.50.21523940.9550.251
2.5-2.60.15120050.9770.1751
2.6-30.06755320.9960.0781
3-3.40.03132510.9990.0361
3.4-3.80.02319960.9990.0271
3.8-4.20.0213550.9990.0241
4.2-4.60.0218800.9990.0251
4.6-100.0226170.9990.0231
10-200.0332400.9970.0381

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XSCALEdata scaling
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.05 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 1285 5.04 %
Rwork0.1932 --
obs0.195 25510 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 14 78 1315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071255
X-RAY DIFFRACTIONf_angle_d1.0891698
X-RAY DIFFRACTIONf_dihedral_angle_d13.094479
X-RAY DIFFRACTIONf_chiral_restr0.067195
X-RAY DIFFRACTIONf_plane_restr0.004218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2880.50971150.51022161X-RAY DIFFRACTION79
2.288-2.39190.37821420.29552667X-RAY DIFFRACTION97
2.3919-2.51780.27111510.22492806X-RAY DIFFRACTION100
2.5178-2.67510.23551430.20152747X-RAY DIFFRACTION100
2.6751-2.8810.22391470.18562773X-RAY DIFFRACTION100
2.881-3.16980.20561490.18912795X-RAY DIFFRACTION100
3.1698-3.62570.25121450.18342737X-RAY DIFFRACTION100
3.6257-4.55770.20431470.1622778X-RAY DIFFRACTION100
4.5577-19.050.19061460.18022761X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.98010.7012-1.35967.3581-2.86256.6371-0.02210.28320.3321-0.02180.011-0.3335-0.35340.05160.01670.331-0.0264-0.01850.230.00130.260318.242427.927340.3691
22.39892.78261.48233.3611.74910.92210.75940.9491-0.7426-1.2430.0369-1.15090.6560.4723-0.77381.45760.3271-0.33840.8691-0.02821.727119.482511.05227.2187
38.87280.4333-0.7167.98763.28825.98150.0442-0.34690.27140.0526-0.01020.3484-0.2079-0.0601-0.05810.30180.0302-0.00010.2369-0.00480.226613.0742-3.725935.3309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 152 )

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