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- PDB-8cbx: Crystal Structure of Anti-Cortisol Fab fragment -

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Basic information

Entry
Database: PDB / ID: 8cbx
TitleCrystal Structure of Anti-Cortisol Fab fragment
Components
  • anti-cortisol (17) Fab (heavy chain)
  • anti-cortisol (17) Fab (light chain)
KeywordsIMMUNE SYSTEM / Fab / cortisol / hapten / glucocorticoid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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 16, 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

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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)48,4683
Polymers48,2742
Non-polymers1941
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-26 kcal/mol
Surface area19920 Å2
Unit cell
Length a, b, c (Å)80.015, 80.015, 254.161
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: PEG3350, citric acid / PH range: 4.2

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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, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2→40.01 Å / Num. obs: 33324 / % possible obs: 99.53 % / Redundancy: 17.6 % / Biso Wilson estimate: 40.19 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1166 / Net I/σ(I): 13.3
Reflection shellResolution: 2.002→2.074 Å / Rmerge(I) obs: 1.051 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 3095 / CC1/2: 0.715 / CC star: 0.913

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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→40.01 Å / SU ML: 0.2483 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 1730 5.19 %
Rwork0.2233 31588 -
obs0.2241 33318 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.73 Å2
Refinement stepCycle: LAST / Resolution: 2→40.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 13 142 3467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863408
X-RAY DIFFRACTIONf_angle_d1.07254629
X-RAY DIFFRACTIONf_chiral_restr0.0629509
X-RAY DIFFRACTIONf_plane_restr0.0061587
X-RAY DIFFRACTIONf_dihedral_angle_d15.40231219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.31031400.31752413X-RAY DIFFRACTION95.01
2.06-2.130.3531520.31972556X-RAY DIFFRACTION99.6
2.13-2.20.31671440.29832585X-RAY DIFFRACTION100
2.2-2.290.32541440.28052590X-RAY DIFFRACTION100
2.29-2.40.29561610.27392579X-RAY DIFFRACTION100
2.4-2.520.29021560.2722599X-RAY DIFFRACTION100
2.52-2.680.28671210.25642643X-RAY DIFFRACTION100
2.68-2.890.28361470.26382625X-RAY DIFFRACTION100
2.89-3.180.251330.24712652X-RAY DIFFRACTION100
3.18-3.640.25121390.22312698X-RAY DIFFRACTION100
3.64-4.580.19791330.18392725X-RAY DIFFRACTION100
4.58-40.010.18581600.18462923X-RAY DIFFRACTION99.87
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)
14.072146908250.528886349531-0.7097799393636.07425335842-0.1830563118682.74525118307-0.1124810684860.835179577767-0.36343669008-1.403654944850.3525121594230.6839512141340.53609500161-0.148207651407-0.1524231898010.57646244175-0.133765512429-0.1376782194990.545795031229-0.008921882405980.27851067149616.94921681722.537757166133.405076828
21.38305995527-0.564767810621-0.4488744150075.21426898937-0.8905787981522.00773300178-0.000502693536790.197308194324-0.3629981645240.05629247873470.04537475146180.6281822261930.119789870493-0.480898844708-0.002497703845990.324583783438-0.138234300470.01326258991520.3632542166350.01653177863390.34519075337815.048282765220.4601047405142.889407356
34.816183992450.226408436363-1.994738657921.50976982058-0.9026897820051.999630258950.2220146010050.247599051192-0.00688664942652-0.178484165267-0.1789813172660.04750101351070.1545091593030.0398872292101-0.04045925316550.429554062966-0.0625030406023-0.02258158989460.328977811685-0.03650776052770.13233441819936.360435130720.2637436111131.265618943
47.5909877903-3.67649145184-2.935397264775.323223988741.697254084965.010778108940.03327483579771.23618772413-0.355719555085-0.573774571647-0.08816801042470.3774185201560.543471122442-0.578401976230.04261961341220.505874303262-0.1496369451260.06401613413480.5029992468660.04138775809380.34268805083344.631014079225.1387739995120.244584183
57.18097286082-4.50633284922-2.111377116664.716399103412.216217342891.03838827233-0.03030870019140.440247599981-0.325086013522-0.18559847569-0.04171405706320.01211410866710.0615313451563-0.5384145065420.09335017530880.528239678737-0.1748615272520.1106459325640.5291348028870.1014656595380.3664816633738.508931855724.2560237865129.497274726
68.11726804181-0.593504474065-0.8606396488263.66224765573-2.491472550264.752768154160.4796076968081.34763536596-1.47114798817-1.16321983595-0.808337849502-0.1103473026630.794755623152-0.2649757205280.3077353202260.9202301779880.05497803037040.1340254264880.57583709408-0.1143474926410.57242794008754.162251786115.7824970035117.929384127
78.63147169077-2.43391589467-5.325212881726.536801709542.115921188246.558978339310.8036370828120.8216948211170.605476187813-0.836822972023-0.2873556926030.650339518399-0.410517335578-0.932821050066-0.4631216924170.561281479303-0.03072030984220.01182891361750.7936000656240.2225299086460.44392779908445.723521311330.0649498506115.970680861
89.77433273656-4.62908602202-6.332279676536.196361519554.581733553194.78741227902-0.362224720568-0.4964372230080.3141397335570.2865865756340.699969418295-0.269915375560.6827742021820.850768739273-0.3697700500770.4849693460840.039798917990.01641073870060.7255385524780.126935983340.37795918526258.499042725327.8016550236117.406394654
92.917489076751.252516693790.08015088319124.50660069984-1.142335245292.836949867840.0312652853385-0.0568737493881-0.4030243286320.135765571064-0.142356802014-0.3941679436180.559545712040.08855353812880.05779671755140.627825736289-0.1807396114530.05343273440060.234378750698-0.02626709880650.55739713749626.26275528032.54921408659148.671389584
102.906090441420.9735000455040.5298762112375.193505351710.005998232285041.16952597617-0.1652531476340.111655243519-0.687852275372-0.1158399009380.09952708814220.01783221631720.674150213746-0.1675727026190.01351357648790.775266844637-0.2357653064730.0446152599260.301892964579-0.04424952446290.68510889847821.6357628758-1.4592258413147.947750211
113.582941276980.417071174008-2.404938979080.444062545814-0.830677261282.52867852325-0.255327244657-0.0303902248852-0.407654005763-0.177165708037-0.200749144286-0.1287997345910.3048832741990.3539496113150.4660826327190.644433919681-0.0643919012494-0.01098591163140.421470162410.07245584432840.35793681140644.425611638513.4840210803137.337738907
124.415478961511.10546788194-0.5774528815044.98490389346-0.1260257768323.054042863090.0590060438839-0.134583328588-0.16691794760.752426282551-0.345586235376-0.169143802630.6062640036730.4870231809720.291033267420.730981893623-0.04874405872430.02045261064830.5063975485250.1155486463470.30087014307852.728557358719.5993625783136.922042944
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 88 )LA19 - 8819 - 88
33chain 'L' and (resid 89 through 125 )LA89 - 12589 - 125
44chain 'L' and (resid 126 through 152 )LA126 - 152126 - 152
55chain 'L' and (resid 153 through 171 )LA153 - 171153 - 171
66chain 'L' and (resid 172 through 185 )LA172 - 185172 - 185
77chain 'L' and (resid 186 through 201 )LA186 - 201186 - 201
88chain 'L' and (resid 202 through 211 )LA202 - 211202 - 211
99chain 'H' and (resid 1 through 51 )HB1 - 511 - 51
1010chain 'H' and (resid 52 through 105 )HB52 - 10552 - 105
1111chain 'H' and (resid 106 through 140 )HB106 - 140106 - 140
1212chain 'H' and (resid 141 through 221 )HB141 - 221141 - 221

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