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- PDB-6itq: Crystal structure of cortisol complexed with its nanobody at pH 10.5 -

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Basic information

Entry
Database: PDB / ID: 6itq
TitleCrystal structure of cortisol complexed with its nanobody at pH 10.5
Componentsanti-cortisol camelid antibody
KeywordsIMMUNE SYSTEM / Cortisol / Complex / Nanobody / Camelid antibody
Function / homologyChem-HCY
Function and homology information
Biological speciesCamelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.526 Å
AuthorsDing, Y. / Ding, L.L. / Wang, Z.Y. / Zhong, P.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)31470764 China
National Science Foundation (China)91527305 China
CitationJournal: Febs Lett. / Year: 2019
Title: Structural insights into the mechanism of single domain VHH antibody binding to cortisol.
Authors: Ding, L. / Wang, Z. / Zhong, P. / Jiang, H. / Zhao, Z. / Zhang, Y. / Ren, Z. / Ding, Y.
History
DepositionNov 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: anti-cortisol camelid antibody
B: anti-cortisol camelid antibody
C: anti-cortisol camelid antibody
D: anti-cortisol camelid antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,76210
Polymers55,1204
Non-polymers1,6426
Water10,070559
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, 1:1 binding, isothermal titration calorimetry, 1:1 binding
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-18 kcal/mol
Surface area22160 Å2
Unit cell
Length a, b, c (Å)93.870, 48.816, 109.333
Angle α, β, γ (deg.)90.000, 110.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
anti-cortisol camelid antibody


Mass: 13780.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-HCY / (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione / CORTISOL


Mass: 362.460 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 2M Ammonium sulfate, 0.1M CAPS/Sodium hydroxide pH 10.5, 0.2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.526→43.92 Å / Num. obs: 68100 / % possible obs: 96.7 % / Redundancy: 6.3 % / CC1/2: 0.916 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.095 / Rrim(I) all: 0.23 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.53-1.616.60.85298860.6990.3720.93296.9
4.83-43.926.50.15623010.9680.0670.1798.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.53 Å43.92 Å
Translation1.53 Å43.92 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.6.2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K1K

3k1k


Resolution: 1.526→43.917 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.92
RfactorNum. reflection% reflection
Rfree0.2562 3256 4.83 %
Rwork0.2226 --
obs0.2243 67390 95.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.38 Å2 / Biso mean: 16.6123 Å2 / Biso min: 3.59 Å2
Refinement stepCycle: final / Resolution: 1.526→43.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3751 0 114 559 4424
Biso mean--17.19 26.03 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063947
X-RAY DIFFRACTIONf_angle_d0.9135358
X-RAY DIFFRACTIONf_chiral_restr0.061562
X-RAY DIFFRACTIONf_plane_restr0.004669
X-RAY DIFFRACTIONf_dihedral_angle_d13.1742224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5264-1.54920.2711440.26672639278392
1.5492-1.57340.27541400.24082763290394
1.5734-1.59920.26911320.24842779291195
1.5992-1.62680.27451370.24852760289796
1.6268-1.65640.29931360.24362823295996
1.6564-1.68820.22481400.22762777291796
1.6882-1.72270.26991450.2272773291896
1.7227-1.76010.24951260.22762812293895
1.7601-1.80110.29661560.22822641279793
1.8011-1.84610.29391370.22212836297397
1.8461-1.8960.29761300.23632775290595
1.896-1.95180.38711130.33262527264085
1.9518-2.01480.24881200.21332812293297
2.0148-2.08680.2561350.21632808294396
2.0868-2.17040.24041460.20432864301098
2.1704-2.26920.30811430.25412663280692
2.2692-2.38880.24291550.22552879303498
2.3888-2.53840.25591430.222711285493
2.5384-2.73440.27831560.22122897305399
2.7344-3.00950.22041660.2162900306699
3.0095-3.44490.20861390.19892902304199
3.4449-4.33960.21831590.18022899305898
4.3396-43.93510.25421580.21572894305295

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