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- PDB-9f00: Complex between D-SH2 domain of ABL with monobody DAM27 -

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Basic information

Entry
Database: PDB / ID: 9f00
TitleComplex between D-SH2 domain of ABL with monobody DAM27
Components
  • monobody DAM27
  • synthetic D-SH2 domain
KeywordsPROTEIN BINDING / Complex / monobody / SH2 domain / mirror-image phage display / D-protein
Function / homologypolypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsEssen, L.-O. / Hantschel, O. / Schmidt, N. / Korf, L.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2016-CoG 682311European Union
CitationJournal: Nat Commun / Year: 2024
Title: Development of mirror-image monobodies targeting the oncogenic BCR::ABL1 kinase.
Authors: Schmidt, N. / Kumar, A. / Korf, L. / Dinh-Fricke, A.V. / Abendroth, F. / Koide, A. / Linne, U. / Rakwalska-Bange, M. / Koide, S. / Essen, L.O. / Vazquez, O. / Hantschel, O.
History
DepositionApr 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: synthetic D-SH2 domain
B: synthetic D-SH2 domain
D: monobody DAM27
C: monobody DAM27


Theoretical massNumber of molelcules
Total (without water)43,0364
Polymers43,0364
Non-polymers00
Water23413
1
A: synthetic D-SH2 domain
C: monobody DAM27


Theoretical massNumber of molelcules
Total (without water)21,5182
Polymers21,5182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-7 kcal/mol
Surface area10130 Å2
2
B: synthetic D-SH2 domain
D: monobody DAM27


Theoretical massNumber of molelcules
Total (without water)21,5182
Polymers21,5182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-6 kcal/mol
Surface area10520 Å2
Unit cell
Length a, b, c (Å)111.326, 111.326, 205.749
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein synthetic D-SH2 domain


Mass: 11205.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: D-configured SH2 domain from human ABL, isoform IB / Source: (synth.) synthetic construct (others)
#2: Antibody monobody DAM27


Mass: 10312.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 4.28 Å3/Da / Density % sol: 71.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.8 M tri-Sodium citrate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.9→48.96 Å / Num. obs: 17398 / % possible obs: 100 % / Redundancy: 28.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.065 / Rrim(I) all: 0.258 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-3.0828.73.7831.227440.6110.9953.91399.9
8.71-48.96230.04851.376610.0130.0599.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
STARANISOdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→48.96 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 868 5.02 %
Rwork0.2094 --
obs0.2117 17286 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.91→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 0 13 3007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013082
X-RAY DIFFRACTIONf_angle_d1.3434204
X-RAY DIFFRACTIONf_dihedral_angle_d11.176789
X-RAY DIFFRACTIONf_chiral_restr0.087464
X-RAY DIFFRACTIONf_plane_restr0.01537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.090.37941390.36472649X-RAY DIFFRACTION99
3.09-3.330.34921440.29612661X-RAY DIFFRACTION100
3.33-3.660.31751400.24852696X-RAY DIFFRACTION100
3.66-4.190.28091310.20912725X-RAY DIFFRACTION100
4.19-5.280.19041620.16032746X-RAY DIFFRACTION100
5.28-48.960.24061520.19082941X-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)
11.9981.67730.0716.80861.11041.8283-0.0551-0.2633-0.3074-0.03760.0086-0.39310.08510.11330.00040.7634-0.12610.13430.64030.02050.7428-68.3725-13.2381-31.143
24.4792-0.8255-2.52473.4411.2294.71460.2692-0.2859-0.175-0.0408-0.1444-0.32440.16070.5356-0.00060.7815-0.10330.06920.6771-0.07080.7262-46.73946.9529-41.2838
34.35490.5205-1.41613.60730.61845.36170.6257-1.17670.29120.8714-0.4180.0884-0.24950.6274-0.00041.0829-0.33640.09691.215-0.22040.7561-54.603612.3385-16.2385
44.0233-0.5119-1.71993.78410.74163.89560.23250.14650.68620.3548-0.02220.5947-0.517-0.5392-0.00010.80980.01460.1780.726-0.05771.0024-77.694311.4388-33.3159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 6 through 98 )
2X-RAY DIFFRACTION2chain 'D' and (resid 3 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 239 )
4X-RAY DIFFRACTION4chain 'B' and (resid 141 through 239 )

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