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- PDB-7ooi: Anti-EphA1 JD1 VH domain -

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Basic information

Entry
Database: PDB / ID: 7ooi
TitleAnti-EphA1 JD1 VH domain
ComponentsJD1 VH domain
KeywordsIMMUNE SYSTEM / VH domain / EphA1
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsEreno-Orbea, J. / Nilvebrant, J. / Sidhu, S. / Julien, J.P.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Banting Postdoctoral Fellowships Canada
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Systematic Engineering of Optimized Autonomous Heavy-Chain Variable Domains.
Authors: Nilvebrant, J. / Ereno-Orbea, J. / Gorelik, M. / Julian, M.C. / Tessier, P.M. / Julien, J.P. / Sidhu, S.S.
History
DepositionMay 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: JD1 VH domain
B: JD1 VH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8154
Polymers27,6232
Non-polymers1922
Water2,108117
1
A: JD1 VH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9072
Polymers13,8111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: JD1 VH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9072
Polymers13,8111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.210, 60.210, 168.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-345-

HOH

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Components

#1: Antibody JD1 VH domain


Mass: 13811.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.2 M ammonium sulphate, 10% glycerol, 0.1 M phosphate citrate (pH 4.2) and 20% (w/v) polyethyleneglycol (PEG) 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.15→42.58 Å / Num. obs: 17674 / % possible obs: 99.9 % / Redundancy: 13.552 % / Biso Wilson estimate: 41.641 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.26 / Rrim(I) all: 0.27 / Χ2: 0.791 / Net I/σ(I): 10.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.2812.7162.2842.0127510.7242.37799.7
2.28-2.4313.3661.6912.9326290.8241.756100
2.43-2.6313.9891.1974.2724680.9011.242100
2.63-2.8814.2190.7137.0322680.9640.74100
2.88-3.2214.2390.3811.1420570.9850.394100
3.22-3.7113.9060.18617.7518540.9950.19399.9
3.71-4.5413.490.10924.0815920.9970.11399.9
4.54-6.3813.1130.09125.612700.9980.095100
6.38-6.3812.0050.06827.097850.9990.07199.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXv1.14refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B9V

3b9v


Resolution: 2.28→42.58 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.297 --
Rwork0.269 --
obs-14893 99.85 %
Displacement parametersBiso max: 97.03 Å2 / Biso mean: 36.4973 Å2 / Biso min: 10.02 Å2
Refinement stepCycle: LAST / Resolution: 2.28→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 10 117 2069

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