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- PDB-8cby: Crystal Structure of Anti-cortisol Fab in Complex with Cortisol -

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Basic information

Entry
Database: PDB / ID: 8cby
TitleCrystal Structure of Anti-cortisol Fab in Complex with Cortisol
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 / Chem-HCY
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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

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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)48,6363
Polymers48,2742
Non-polymers3621
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-32 kcal/mol
Surface area19460 Å2
Unit cell
Length a, b, c (Å)79.937, 79.937, 253.453
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-HCY / (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione / CORTISOL


Mass: 362.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: PEG3350, Ammonium citrate / 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, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.27→42.24 Å / Num. obs: 22992 / % possible obs: 99.7 % / Redundancy: 32.6 % / Biso Wilson estimate: 37.88 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.175 / Net I/σ(I): 13.4
Reflection shellResolution: 2.27→2.355 Å / Rmerge(I) obs: 1.41 / Num. unique obs: 2207 / CC1/2: 0.819 / CC star: 0.949

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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: 2.27→42.24 Å / SU ML: 0.2908 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7914
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2303 1164 5.06 %
Rwork0.2022 21824 -
obs0.2036 22992 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.93 Å2
Refinement stepCycle: LAST / Resolution: 2.27→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 26 146 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893429
X-RAY DIFFRACTIONf_angle_d1.16154673
X-RAY DIFFRACTIONf_chiral_restr0.0825517
X-RAY DIFFRACTIONf_plane_restr0.0079591
X-RAY DIFFRACTIONf_dihedral_angle_d16.14111222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.380.36711540.30112595X-RAY DIFFRACTION98.5
2.38-2.50.34171540.26792661X-RAY DIFFRACTION100
2.5-2.660.26211330.24772685X-RAY DIFFRACTION99.96
2.66-2.860.25691490.24152664X-RAY DIFFRACTION100
2.86-3.150.2751350.23252707X-RAY DIFFRACTION100
3.15-3.610.22711410.20552738X-RAY DIFFRACTION100
3.61-4.550.2031340.16932788X-RAY DIFFRACTION100
4.55-42.240.17481640.16462986X-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)
12.401159721-0.4116802360.0106209582.8717405390.7112211921.111148407-0.002122143-0.374150187-0.1786962080.758264762-0.148423659-0.3847410950.1417006670.172056450.0124400110.3019158550.006969806-0.0305615680.3489957790.0303230230.229301887-16.76298985822.3499523083-6.10595789417
20.8561594180.291227478-0.009644243.5653814520.74212410.8817496220.001053706-0.087231549-0.2407685340.010461975-0.01834236-0.2482339790.1120166820.1640710880.0148232150.2055896480.0299735490.000293860.200445130.0181206350.202002819-16.570859602220.3200723381-13.7471785872
33.0611704780.503333118-0.7366096911.712712377-0.1507692861.278049532-0.040548078-0.228280992-0.0851055180.112632424-0.015319198-0.2428231160.0616016190.1127911320.0315590830.2649809150.0254301170.032139540.215656535-0.0131509070.227687119-44.810860496923.407705652.64192506379
42.516583673-0.996343178-1.2643525843.1237121041.1976832883.603424751-0.134533253-0.568546978-0.1946684190.2193840890.055987545-0.1427495030.2537879370.3204848780.0197360330.2867685710.0273200060.0181845040.280949316-0.0064208050.216740277-51.125446336724.04095612949.78913288826
52.037147177-0.808973414-0.4415121722.2338958810.4464982662.1706634080.164310280.247512282-0.231217526-0.484003752-0.2198364650.6422738940.23608525-0.1510031640.126775160.4250959250.077568576-0.0518778870.242376503-0.0540377090.430638513-28.06716337131.50193318304-25.5640152384
61.841633955-0.343226296-0.209976293.5978401150.4209959672.0064458540.000712497-0.114274094-0.276142119-0.016121631-0.0246230680.1198649520.2582765870.1581963450.0832429750.3166263870.0644435790.0082661940.1996288530.0182879660.365900913-20.2663161167-1.14218969033-18.5076329223
72.114420642-0.256968064-0.6850929473.1089081960.3202506160.242175967-0.173120602-0.00799504-0.698916113-0.037184182-0.3733121630.6410135020.535004572-0.2105655290.1276251440.3802209530.011449017-0.0048057030.235766374-0.0304512920.516201552-28.2913116703-4.2940008468-16.5432414022
81.475316250.2025803260.9029215681.7829428210.2665609221.5506999530.0736051480.393187545-0.13085094-0.268960188-0.072044489-0.312171917-0.0257065390.141109050.005696230.3217815190.064257930.0184708460.2173713920.0047104360.398255987-17.58803460967.04678256301-22.6736235517
91.6331979670.089127979-0.229027272-0.077514335-0.0405958840.049461994-0.201188201-0.076640011-0.6824956990.007646269-0.1012992690.0416200660.2145723770.0096012040.2411048950.3871319580.02748550.0510520060.231625814-0.0618365150.482900868-34.57998994994.61123447161-15.6679865109
102.718698995-0.274738068-0.4337376260.116537397-0.517211073.496629096-0.0528250070.1308177010.470083040.229739261-0.245440810.195450569-0.417470616-0.313463990.2721362220.2724962310.041206629-0.0168927350.231194343-0.0208390190.267305371-56.856880053726.1709677495-1.92918295487
110.75584115-0.230197879-0.2826666091.78050319-0.0685121890.689672978-0.0032691280.055583662-0.052504508-0.589639173-0.061806278-0.2295957360.119451579-0.080411320.045737680.4222498460.0316261740.0424514410.241780767-0.0187829420.250676804-49.580398691317.65867534-10.1130244464
122.992454280.6467263290.0773703232.6323674960.5544237940.954804132-0.159692345-0.150956474-0.1942963610.0033394060.187603534-0.41658064-0.13452195-0.238114013-0.0192995680.3863887060.0009031240.0900671650.2259168060.0179046470.313014024-44.887669952918.6539223081-7.38096927495
132.670892965-0.0649367210.1081298634.229156846-0.7318415731.099398016-0.136516802-0.1401638190.048784372-0.0265043080.125565356-0.3066191370.122576194-0.1395035440.066976610.3740317350.040812510.0607455730.259690712-0.0008903070.221222618-50.486741308623.4118531033-7.55469606181
142.247169453-0.978925041-0.6078595544.7804858031.6689864051.042838523-0.0960857770.120546994-0.009859114-1.000278278-0.013189870.3328435030.364420498-0.2155626920.1483177460.6049251510.037529136-0.0072065760.320786428-0.0733220530.286229815-56.073218265720.5894290395-13.6810389521
151.798171338-0.2139752250.7185589754.1764233250.183281891.46900501-0.1243841220.117404839-0.042225501-0.552012652-0.0698799380.534114550.224735288-0.3980380030.1907838910.5187998620.043745277-0.1110310730.376206319-0.1041088550.406973019-60.586301682518.4984745175-9.17039623931
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 171 )LA111 - 171111 - 171
44chain 'L' and (resid 172 through 211 )LA172 - 211172 - 211
55chain 'H' and (resid 1 through 33 )HB1 - 331 - 33
66chain 'H' and (resid 34 through 76 )HB34 - 7634 - 76
77chain 'H' and (resid 77 through 91 )HB77 - 9177 - 91
88chain 'H' and (resid 92 through 105 )HB92 - 10592 - 105
99chain 'H' and (resid 106 through 125 )HB106 - 125106 - 125
1010chain 'H' and (resid 126 through 140 )HB126 - 140126 - 140
1111chain 'H' and (resid 141 through 163 )HB141 - 163141 - 163
1212chain 'H' and (resid 164 through 179 )HB164 - 179164 - 179
1313chain 'H' and (resid 180 through 193 )HB180 - 193180 - 193
1414chain 'H' and (resid 194 through 208 )HB194 - 208194 - 208
1515chain 'H' and (resid 209 through 221 )HB209 - 221209 - 221

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