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- PDB-2jab: A designed ankyrin repeat protein evolved to picomolar affinity t... -

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Basic information

Entry
Database: PDB / ID: 2jab
TitleA designed ankyrin repeat protein evolved to picomolar affinity to Her2
ComponentsH10-2-G3
KeywordsDE NOVO PROTEIN / HER2 / DARPIN / ANKYRIN REPEAT PROTEIN / MEMBRANE PROTEIN / HUMAN EPIDERMAL GROWTH FACTOR RECEPTOR 2
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZahnd, C. / Wyler, E. / Schwenk, J.M. / Steiner, D. / Lawrence, M.C. / McKern, N.M. / Pecorari, F. / Ward, C.W. / Joos, T.O. / Pluckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A Designed Ankyrin Repeat Protein Evolved to Picomolar Affinity to Her2
Authors: Zahnd, C. / Wyler, E. / Schwenk, J.M. / Steiner, D. / Lawrence, M.C. / Mckern, N.M. / Pecorari, F. / Ward, C.W. / Joos, T.O. / Pluckthun, A.
History
DepositionNov 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 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: H10-2-G3
B: H10-2-G3
C: H10-2-G3


Theoretical massNumber of molelcules
Total (without water)43,8553
Polymers43,8553
Non-polymers00
Water8,791488
1
A: H10-2-G3


Theoretical massNumber of molelcules
Total (without water)14,6181
Polymers14,6181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: H10-2-G3


Theoretical massNumber of molelcules
Total (without water)14,6181
Polymers14,6181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: H10-2-G3


Theoretical massNumber of molelcules
Total (without water)14,6181
Polymers14,6181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)152.080, 52.191, 70.164
Angle α, β, γ (deg.)90.00, 105.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2040-

HOH

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Components

#1: Protein H10-2-G3


Mass: 14618.437 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / 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

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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: 2.88 Å3/Da / Density % sol: 57 %
Crystal growpH: 8.5
Details: PROTEIN: 6 MG/ML IN 20 MM SODIUM PHOSPHATE, 75 MM NACL PH 7.4. PRECIPITANT: 0.1 M TRISHCL (PH 8.5), 2.3 M (NH4)2SO4, 10% GLYCEROL (V/V). ROOM TEMPERATURE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 10, 2004 / Details: AXCO CAPILLARY
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→73.3 Å / Num. obs: 58105 / % possible obs: 98.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.3 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1MJ0 AND 2BKG

1mj0

2bkg


Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.886 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO NCS RESTRAINTS WERE APPLIED DURING THE FINAL STAGES OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2929 5.2 %RANDOM
Rwork0.178 ---
obs0.18 53757 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.4 Å2
2--0.98 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 0 488 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.973827
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9395370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86826.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09215481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.367156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022120
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21412
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21971
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2334
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.84421880
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.65532891
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.35221029
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.4183936
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 188 -
Rwork0.287 3768 -
obs--92.41 %
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)
11.57640.50020.04571.2690.9445.7426-0.0150.0373-0.05160.0590.0973-0.04280.14830.1481-0.0822-0.218-0.00240.02-0.1714-0.0134-0.200358.5526.486-5.269
22.3790.66121.6091.88010.25884.59760.1375-0.0634-0.10820.1811-0.026-0.01340.11370.0362-0.1114-0.2089-0.0342-0.0048-0.1760.0079-0.171741.47712.921-8.069
31.9406-0.1609-0.45430.81310.29734.07310.04160.09660.0422-0.0203-0.0164-0.0345-0.08520.0539-0.0252-0.2399-0.00850.0086-0.2125-0.0008-0.216477.80741.3132.615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 135
2X-RAY DIFFRACTION2B12 - 135
3X-RAY DIFFRACTION3C12 - 136

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