[English] 日本語
Yorodumi
- PDB-4lex: Unliganded crystal structure of mAb7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lex
TitleUnliganded crystal structure of mAb7
Components
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Fab fragment / anti-GCGR / Fab heavy and light chain / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsMurray, J.M. / Mukund, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Inhibitory mechanism of an allosteric antibody targeting the glucagon receptor.
Authors: Mukund, S. / Shang, Y. / Clarke, H.J. / Madjidi, A. / Corn, J.E. / Kates, L. / Kolumam, G. / Chiang, V. / Luis, E. / Murray, J. / Zhang, Y. / Hotzel, I. / Koth, C.M. / Allan, B.B.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Jan 1, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: FAB HEAVY CHAIN
H: FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,6332
Polymers46,6332
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-28 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.069, 84.184, 88.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11H-440-

HOH

-
Components

#1: Antibody FAB HEAVY CHAIN


Mass: 23819.527 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) / Strain (production host): BL21
#2: Antibody FAB LIGHT CHAIN


Mass: 22813.418 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) / Strain (production host): BL21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 30.0% Jeffamine ED-2001 (v/v) at 15 mg/mL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 27181 / % possible obs: 90.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Χ2: 1.041 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.02-2.0950.21927230.961192.8
2.09-2.185.20.1827051.006192.4
2.18-2.275.20.16727331.053192.4
2.27-2.395.30.14827101.023192.1
2.39-2.545.30.13127061.081191.5
2.54-2.745.30.11227191.074191.8
2.74-3.025.30.09827201.133191.4
3.02-3.455.30.08827161.038190.5
3.45-4.355.30.08227151.005189.5
4.35-505.30.06927341.033185.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FVD

1fvd


Resolution: 2.02→49.209 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.24 / Cross valid method: Random / σ(F): 1.36 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1393 5.13 %
Rwork0.1852 --
obs0.187 27166 90.89 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.748 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 101.73 Å2 / Biso mean: 29.8885 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.7216 Å20 Å2-0 Å2
2---0.1035 Å20 Å2
3----1.618 Å2
Refinement stepCycle: LAST / Resolution: 2.02→49.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 0 285 3565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063367
X-RAY DIFFRACTIONf_angle_d1.114588
X-RAY DIFFRACTIONf_chiral_restr0.086526
X-RAY DIFFRACTIONf_plane_restr0.005584
X-RAY DIFFRACTIONf_dihedral_angle_d13.6951198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.090.23251360.18532555269192
2.09-2.17370.23051330.18092579271292
2.1737-2.27260.27021320.18332616274892
2.2726-2.39240.24681150.20252586270192
2.3924-2.54230.26071550.20042562271792
2.5423-2.73860.25321300.2052588271892
2.7386-3.01410.23741550.19122563271891
3.0141-3.45020.21821410.19162579272091
3.4502-4.34650.18551610.16552549271090
4.3465-49.22340.1961350.18092596273186
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)
10.40110.2690.09490.7530.01880.266-0.0382-0.08950.11730.07850.00720.0644-0.0528-0.02960.04550.1040.0078-0.01340.1154-0.0220.13612.072127.314128.0428
20.2690.10990.13780.6737-0.04580.5338-0.00520.010.0428-0.00920.00420.0025-0.00690.1336-0.00690.09920.0080.00180.1787-0.01080.14388.101920.346612.107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN LL1 - 217
2X-RAY DIFFRACTION2CHAIN HH1 - 217

+
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://pdbjlvh1.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