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- PDB-6itp: Crystal structure of cortisol complexed with its nanobody at pH 3.5 -

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Basic information

Entry
Database: PDB / ID: 6itp
TitleCrystal structure of cortisol complexed with its nanobody at pH 3.5
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: 1.572 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2854
Polymers27,5602
Non-polymers7252
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, 1:1 binding to cortisol, isothermal titration calorimetry, 1:1 binding to cortisol
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.043, 95.043, 95.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-446-

HOH

21B-386-

HOH

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Components

#1: Antibody anti-cortisol camelid antibody


Mass: 13780.096 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C21H30O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1M Citric acid pH 3.5, 3M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 40074 / % possible obs: 99.8 % / Redundancy: 39.5 % / Biso Wilson estimate: 13.36 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.013 / Rrim(I) all: 0.081 / Χ2: 0.791 / Net I/σ(I): 4.5 / Num. measured all: 1584876
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.6338.30.6539110.9680.1060.6590.72698.3
1.63-1.6940.40.54139590.9580.0860.5480.786100
1.69-1.7739.50.42940060.9670.0690.4350.869100
1.77-1.8638.50.29139640.9830.0470.2950.961100
1.86-1.98410.20439800.9940.0320.2060.91100
1.98-2.1339.30.14939940.9970.0240.1510.848100
2.13-2.3539.70.11639970.9980.0190.1170.827100
2.35-2.6840.50.08740250.9990.0140.0880.743100
2.68-3.38400.057406010.0090.0580.672100
3.38-5038.30.04417810.0060.0410.57199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.98 Å33.6 Å
Translation3.98 Å33.6 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.8.2phasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K1K

3k1k


Resolution: 1.572→33.603 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.47
RfactorNum. reflection% reflection
Rfree0.2229 1979 4.95 %
Rwork0.1947 --
obs0.1961 39992 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.6 Å2 / Biso mean: 20.1569 Å2 / Biso min: 5.37 Å2
Refinement stepCycle: final / Resolution: 1.572→33.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 112 353 2379
Biso mean--13.49 27.55 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012010
X-RAY DIFFRACTIONf_angle_d1.152730
X-RAY DIFFRACTIONf_chiral_restr0.073286
X-RAY DIFFRACTIONf_plane_restr0.006344
X-RAY DIFFRACTIONf_dihedral_angle_d21.4921136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5719-1.61120.25931440.231727182862100
1.6112-1.65470.27421330.230226872820100
1.6547-1.70340.29641340.227826802814100
1.7034-1.75840.24221500.217926922842100
1.7584-1.82130.23851640.209226712835100
1.8213-1.89420.23361550.205826842839100
1.8942-1.98040.25151420.193827052847100
1.9804-2.08480.25771390.192126832822100
2.0848-2.21540.2221500.18427232873100
2.2154-2.38640.21381550.192126802835100
2.3864-2.62640.23351180.19627502868100
2.6264-3.00630.21911220.196127582880100
3.0063-3.78680.21231480.181327462894100
3.7868-33.61040.17041250.18492836296198

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