[English] 日本語
Yorodumi
- PDB-8cby: Crystal Structure of Anti-cortisol Fab in Complex with Cortisol -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
#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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more