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- PDB-8cc0: Crystal Structure of Anti-cortisol Fab in Complex with Cortisone -

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Basic information

Entry
Database: PDB / ID: 8cc0
TitleCrystal Structure of Anti-cortisol Fab in Complex with Cortisone
Components
  • anti-cortisol (17) Fab (heavy chain)
  • anti-cortisol (17) Fab (light chain)
KeywordsIMMUNE SYSTEM / Fab / cortisol / hapten / glucocorticoid / cortisone
Function / homologyCortisone
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsEronen, V. / Rouvinen, J. / Hakulinen, N.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland322619 Finland
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Structural insight to elucidate the binding specificity of the anti-cortisol Fab fragment with glucocorticoids.
Authors: Eronen, V. / Tullila, A. / Iljin, K. / Rouvinen, J. / Nevanen, T.K. / Hakulinen, N.
History
DepositionJan 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: anti-cortisol (17) Fab (light chain)
H: anti-cortisol (17) Fab (heavy chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6343
Polymers48,2742
Non-polymers3601
Water6,990388
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-31 kcal/mol
Surface area19190 Å2
Unit cell
Length a, b, c (Å)79.411, 79.411, 251.858
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Antibody anti-cortisol (17) Fab (light chain)


Mass: 23276.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody anti-cortisol (17) Fab (heavy chain)


Mass: 24997.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-UQC / Cortisone / (8S,9S,10R,13S,14S,17R)-10,13-dimethyl-17-oxidanyl-17-(2-oxidanylethanoyl)-1,2,6,7,8,9,12,14,15,16-decahydrocyclopenta[a]phenanthrene-3,11-dione / 17alpha,21-Dihydroxypregn-4-ene-3,11,20-trione


Mass: 360.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: PEG3350, Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.85→41.98 Å / Num. obs: 41193 / % possible obs: 99.8 % / Redundancy: 17.9 % / Biso Wilson estimate: 24.41 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.2356 / Net I/σ(I): 12
Reflection shellResolution: 1.85→1.916 Å / Rmerge(I) obs: 1.414 / Num. unique obs: 3991 / CC1/2: 0.76 / CC star: 0.929

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASER1.19.2_4158phasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MHE

5mhe


Resolution: 1.85→41.98 Å / SU ML: 0.2042 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.2381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.209 2165 5.25 %
Rwork0.1905 39073 -
obs0.1915 41187 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.69 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 26 388 3726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853429
X-RAY DIFFRACTIONf_angle_d1.05964673
X-RAY DIFFRACTIONf_chiral_restr0.1257517
X-RAY DIFFRACTIONf_plane_restr0.0069591
X-RAY DIFFRACTIONf_dihedral_angle_d6.6389477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.30531360.32122477X-RAY DIFFRACTION96.53
1.89-1.940.28441490.27242533X-RAY DIFFRACTION100
1.94-1.990.2631580.22252538X-RAY DIFFRACTION100
1.99-2.050.22631440.21092539X-RAY DIFFRACTION99.96
2.05-2.120.25941490.20262548X-RAY DIFFRACTION100
2.12-2.190.24881500.20872558X-RAY DIFFRACTION100
2.19-2.280.26721390.21922575X-RAY DIFFRACTION99.96
2.28-2.380.24151630.20382560X-RAY DIFFRACTION100
2.38-2.510.24991470.20292576X-RAY DIFFRACTION100
2.51-2.670.20761230.19952630X-RAY DIFFRACTION99.96
2.67-2.870.21961470.20722607X-RAY DIFFRACTION100
2.87-3.160.20741290.19692646X-RAY DIFFRACTION100
3.16-3.620.20131410.17232669X-RAY DIFFRACTION100
3.62-4.560.15461310.14962715X-RAY DIFFRACTION100
4.56-41.980.16211590.1722902X-RAY DIFFRACTION99.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.87294393813-2.02503813217-0.3296848689756.723982516060.608614709162.03078118921-0.0696573626925-0.179713599107-0.240656384450.7681173082650.0210568049595-0.1900604611650.2596536294320.1234065631010.03182536846530.221757091564-0.0102113396413-0.05131087109990.2158841479510.0208558665550.0980394437476-17.189445604122.4979355396-6.00186977874
21.94291812347-0.436729394829-0.02180289365344.63581568650.4719561997911.12647288706-0.0312532583468-0.0155759010387-0.127093894507-0.001386188120390.0121644370313-0.515270680916-0.01483032003510.1736738743060.03763021956190.1391390448150.0109781815270.01256981056560.1551196677520.02052780630080.171697863271-13.622566280119.2197107477-15.8366737304
30.286273299128-0.2899046880130.08015394878062.476986115740.6191959014970.3169568418210.00716479908342-0.0407112594039-0.05137705492180.252315144655-0.06332008268390.04492365590090.07518446683460.02480271808140.05451564158870.144970535688-0.001636872424270.00755699273990.1563720669230.01944046602580.137869651877-22.004892547722.1353024608-10.3384218578
46.455941756775.34586611988-0.5573765671034.50076997491-0.3931516030041.73140602073-0.1945702631230.1590735826930.027848088204-0.2284897698270.161924494240.2160663271880.185881811322-0.2382649566650.05432058956950.197904627744-0.000407417793760.02885202142430.199599237173-0.01928008078840.120402900921-57.162881048419.41502343941.70556025675
56.646175658343.22419448439-3.331597754422.99766618306-2.070634947133.25473470067-0.0436922300164-0.682312230243-0.1871073059190.244546971715-0.0537895713148-0.166065780776-0.0358644435520.3067054913550.1254995951320.2227408064270.0660581672240.004849720873130.2117306526380.007402950917540.176158674911-44.396052542824.92605295556.70824921827
65.320527537290.9699946150970.8149943273666.200014644851.108916840730.277897580912-0.2649946501220.0481358611437-0.340165605296-0.2021045823220.126008025667-0.3716303297670.2817607432320.07823488135540.1272271669430.1348296298070.04640468498490.02308868402830.168045735532-0.02703676048080.143814875914-38.258410187624.1387863564-2.44273664111
78.498120107772.45264408353-3.537946346594.5897724823-1.898762210416.83670659643-0.0105757583501-0.822220989301-0.7631941500030.718454527528-0.1639191353350.2014454484070.385371405873-0.0002087672129710.1616496749140.3786348400540.01629308436840.08790746598310.225353774530.05282287979790.267930630113-53.737194922315.54199865289.07384964035
89.053722779413.10473386266-3.167460622866.95119067132-0.8451955956416.774634745470.156899677229-0.5045224576020.2468835943460.304017003002-0.0758942982387-0.1602304262390.07406963801620.292865836248-0.06309220783230.2229679020150.04254007601160.004361126873770.173913125264-0.04126665697540.11336309295-50.625532580228.955465971810.2885838385
92.21438727357-0.0561022055616-0.3269891537393.0140446927-0.09471616378672.213584339110.05083233185090.0436176439715-0.0664753508761-0.14288650103-0.0781444435410.07734962411570.150005549083-0.007624316775890.03307495584740.1777428914010.0269785127657-0.01632870970690.1047129071590.00512127314980.176493100739-23.68321650660.398563345295-20.7185790423
101.74135064761-0.2954671494470.3158451980150.2212999810220.1207394653790.2465752050770.0617110264503-0.0449717423045-0.1342865591680.00122475779029-0.1033470183060.1591187967510.07374163747220.02896182892940.03603840714670.25579304850.01243236282720.005460970368070.161650946251-0.02282576830440.282441783351-34.9654788624.47480203811-15.600879149
114.94548090132-0.160597521295-0.8257957838320.150228927415-0.9024325140586.072597105150.0230554893179-0.09204090504370.4895254018920.202512253383-0.1144580986820.191227464757-0.480291838645-0.284803212610.0672144166190.179700899230.0273820973705-0.00433285258060.180012606619-0.001585372825630.161707058705-57.449419726726.1257727781-1.89653965241
122.72986659121-1.474480154370.1214249456.4453108682-0.3782693022711.007014268960.05549100338740.12461771887-0.144343905861-0.40203812253-0.1143622886720.2541850505450.123764658576-0.1493728357950.07606872691070.265112957974-0.003673418900320.005076655032810.195162047133-0.01642119059310.121122696365-52.500463460319.4148596652-9.69495871488
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 1 through 18 )LA1 - 181 - 18
22chain 'L' and (resid 19 through 74 )LA19 - 7419 - 74
33chain 'L' and (resid 75 through 110 )LA75 - 11075 - 110
44chain 'L' and (resid 111 through 125 )LA111 - 125111 - 125
55chain 'L' and (resid 126 through 152 )LA126 - 152126 - 152
66chain 'L' and (resid 153 through 171 )LA153 - 171153 - 171
77chain 'L' and (resid 172 through 185 )LA172 - 185172 - 185
88chain 'L' and (resid 186 through 211 )LA186 - 211186 - 211
99chain 'H' and (resid 1 through 105 )HB1 - 1051 - 105
1010chain 'H' and (resid 106 through 125 )HB106 - 125106 - 125
1111chain 'H' and (resid 126 through 140 )HB126 - 140126 - 140
1212chain 'H' and (resid 141 through 221 )HB141 - 221141 - 221

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