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- PDB-8cc1: Crystal Structure of Anti-cortisol Fab in Complex with Prednisolone -

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Basic information

Entry
Database: PDB / ID: 8cc1
TitleCrystal Structure of Anti-cortisol Fab in Complex with Prednisolone
Components
  • anti-cortisol (17) Fab (heavy chain)
  • anti-cortisol (17) Fab (light chain)
KeywordsIMMUNE SYSTEM / Fab / cortisol / hapten / glucocorticoid / prednisolone
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / prednisolone
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-32 kcal/mol
Surface area19340 Å2
Unit cell
Length a, b, c (Å)79.604, 79.604, 252.583
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-TUA / prednisolone / (11alpha)-11,17,21-trihydroxypregna-1,4-diene-3,20-dione


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


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.71 %
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: 2→42.1 Å / Num. obs: 33018 / % possible obs: 99.93 % / Redundancy: 18.5 % / Biso Wilson estimate: 26.08 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.3112 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.073 Å / Rmerge(I) obs: 1.926 / Num. unique obs: 3198 / CC1/2: 0.735 / CC star: 0.92 / % possible all: 99.97

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Processing

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

5mhe


Resolution: 2→42.1 Å / SU ML: 0.2089 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.8012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 1712 5.19 %
Rwork0.195 31294 -
obs0.1968 33004 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.1 Å2
Refinement stepCycle: LAST / Resolution: 2→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 26 235 3573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763429
X-RAY DIFFRACTIONf_angle_d1.01124673
X-RAY DIFFRACTIONf_chiral_restr0.0686517
X-RAY DIFFRACTIONf_plane_restr0.0073591
X-RAY DIFFRACTIONf_dihedral_angle_d14.68481222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.28551430.25752520X-RAY DIFFRACTION99.96
2.06-2.130.31711510.24592538X-RAY DIFFRACTION100
2.13-2.20.28361470.23012543X-RAY DIFFRACTION100
2.2-2.290.32561450.22432541X-RAY DIFFRACTION99.96
2.29-2.390.25621590.22182553X-RAY DIFFRACTION100
2.39-2.520.28191390.21792564X-RAY DIFFRACTION100
2.52-2.680.24151290.20922591X-RAY DIFFRACTION99.93
2.68-2.890.24021440.22132595X-RAY DIFFRACTION100
2.89-3.180.2551260.20452627X-RAY DIFFRACTION100
3.18-3.640.22891390.18882660X-RAY DIFFRACTION100
3.64-4.580.17981330.15442682X-RAY DIFFRACTION99.89
4.58-42.10.17321570.17032880X-RAY DIFFRACTION99.67
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)
11.381425030.192146728-0.1095888551.469253410.8453220361.4427481140.064192117-0.213046896-0.3339909380.829663918-0.099067814-0.4890648260.1525017890.007944196-0.0240458950.229028727-0.008694456-0.0576934060.2237634380.0613997010.216359999-17.0880914622.51829069-6.080981543
20.5473189460.407325384-0.097415522.7658888660.8366681930.8143188850.038749426-0.086312283-0.167410427-0.006824479-0.009869819-0.3668253520.0670448290.121201158-0.0262583380.1928097510.0164648120.0012349050.2152411610.030389450.223537769-16.899323220.4325965-13.72299113
32.3495181930.146746461-1.0974024421.251051721-0.2439467391.160877-0.000658856-0.332583528-0.103124220.224585372-0.042633526-0.0251494960.1935023170.0673887440.0522840980.276840860.0276508740.0178154680.2317036820.0060362550.187117664-48.7612921823.130013145.062625301
43.458378677-0.04963733-1.1409564941.5704909580.7081481442.147147557-0.051697736-0.379104178-0.072146520.2150661980.022195641-0.0148396960.1682390490.1555366560.0109205970.2478744270.037186888-0.0008207450.210738292-0.0060390280.139717686-47.5750869824.206275975.954797236
51.418073027-0.2424661860.0796496842.5890663440.1358552981.4180890590.040511217-0.002734791-0.231912294-0.139873974-0.1074638970.1152502650.26690711-0.0052156940.0625399410.2675199750.0270303770.0026199560.1782117520.0109960260.322976322-24.78643475-0.865338823-20.46332537
60.8966656680.1405582590.678822971.906610455-0.3282025251.491293373-0.0511210220.3904547110.085800695-0.18617340.043438727-0.2346301930.1365961080.0781245390.1031608320.2609223580.026802340.0151218860.217369070.0160685590.398468731-17.892024787.00450194-22.71567192
71.5094180820.102974371-0.579755443-0.25222222-0.1395327990.6373367-0.007578574-0.003411699-0.069920490.049984503-0.067873448-0.0352720590.001341001-0.0932559720.0637681960.2646187410.013121330.0053792990.197080411-0.0099741050.25498697-44.2135168313.34466415-10.08781533
82.0112707380.253524706-0.033460593.5148963-0.1887206650.88066080.0171301470.143532739-0.083558923-0.307316865-0.1333047250.195039980.205906171-0.1257254160.1221826650.3201493550.0171070230.0002473250.248802982-0.0259976350.195461376-52.6405275619.46433186-9.748203172
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 110 )LA19 - 11019 - 110
33chain 'L' and (resid 111 through 152 )LA111 - 152111 - 152
44chain 'L' and (resid 153 through 211 )LA153 - 211152 - 211
55chain 'H' and (resid 1 through 91 )HB1 - 911 - 91
66chain 'H' and (resid 92 through 105 )HB92 - 10592 - 105
77chain 'H' and (resid 106 through 140 )HB106 - 140106 - 140
88chain 'H' and (resid 141 through 221 )HB141 - 221141 - 221

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