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- PDB-7eq3: Apo diabody form of CRH2-directed antibody 9F8 -

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Basic information

Entry
Database: PDB / ID: 7eq3
TitleApo diabody form of CRH2-directed antibody 9F8
Components9F8 diabody
KeywordsIMMUNE SYSTEM / Leptin receptor / antagonist
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsYan, L.
CitationJournal: To Be Published
Title: Tall cytokine receptor signaling fine-tuning through dimer geometric reconstitution
Authors: Yan, L.
History
DepositionApr 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 9F8 diabody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0742
Polymers25,0151
Non-polymers591
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.806, 106.806, 50.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody 9F8 diabody


Mass: 25014.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH 8.0, 0.2M Ammonium acetate and 16% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.87→46.25 Å / Num. obs: 7564 / % possible obs: 91.3 % / Redundancy: 8.9 % / CC1/2: 0.75 / Net I/σ(I): 9.7
Reflection shellResolution: 2.87→2.98 Å / Num. unique obs: 621 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V6O

3v6o


Resolution: 2.87→46.25 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 384 5.08 %
Rwork0.2381 7177 -
obs0.2384 7561 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.71 Å2 / Biso mean: 47.9912 Å2 / Biso min: 22.8 Å2
Refinement stepCycle: final / Resolution: 2.87→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 0 0 1746
Num. residues----229
LS refinement shellResolution: 2.87→3.29 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3951 108 -
Rwork0.3191 2272 -
obs--94 %

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