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- PDB-7omn: Anti-EphA1 JD1-1 VH domain -

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Basic information

Entry
Database: PDB / ID: 7omn
TitleAnti-EphA1 JD1-1 VH domain
ComponentsJD1-1 VH domain
KeywordsIMMUNE SYSTEM / VH domain / EphA1
Function / homologyIMIDAZOLE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 24, 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: JD1-1 VH domain
B: JD1-1 VH domain
C: JD1-1 VH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,56810
Polymers41,0613
Non-polymers5077
Water5,567309
1
A: JD1-1 VH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9174
Polymers13,6871
Non-polymers2303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: JD1-1 VH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8253
Polymers13,6871
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: JD1-1 VH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8253
Polymers13,6871
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.870, 131.870, 49.679
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Antibody JD1-1 VH domain


Mass: 13687.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 3.04 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NaCl, 1 M K2HPO4 and 0.1 M Imidazole (pH 7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.7→19.839 Å / Num. obs: 51573 / % possible obs: 94.5 % / Redundancy: 15.708 % / Biso Wilson estimate: 29.354 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.068 / Χ2: 0.886 / Net I/σ(I): 28.98 / Num. measured all: 810118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.85.6010.7361.9139587869070680.7150.81181.3
1.8-1.939.130.4314.6968595821175130.9650.45691.5
1.93-2.0815.7040.28810.06117450763774790.9880.29797.9
2.08-2.2719.5010.20117.42128414705765850.9950.20793.3
2.27-2.5420.1940.12626.44128836638263800.9980.129100
2.54-2.9220.6230.07642.04116890566856680.9990.078100
2.92-3.5619.6170.04665.33947494830483010.048100
3.56-4.9619.2640.03386.85730103793379010.03499.9
4.96-19.83918.8440.03190.32425872303226010.03298.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B9V

3b9v


Resolution: 1.7→19.839 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 1961 3.81 %
Rwork0.2031 49500 -
obs0.2038 51461 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.11 Å2 / Biso mean: 25.6869 Å2 / Biso min: 12.22 Å2
Refinement stepCycle: final / Resolution: 1.7→19.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 36 309 3219
Biso mean--26.37 31.96 -
Num. residues----372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.74230.26771110.2594286577
1.7423-1.78930.30231250.2542313284
1.7893-1.8420.26861310.251336390
1.842-1.90140.3271380.2653355996
1.9014-1.96930.37521290.3559325687
1.9693-2.0480.2241450.20743702100
2.048-2.14110.25161500.21843729100
2.1411-2.25390.24491350.2398334996
2.2539-2.39490.28871450.2257364998
2.3949-2.57940.23981500.21683726100
2.5794-2.83830.20781510.20293750100
2.8383-3.24750.20621480.19943762100
3.2475-4.08560.19291550.17273782100
4.0856-19.8390.16811480.1553876100

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