[English] 日本語
Yorodumi
- PDB-4uin: crystal structure of quinine-dependent Fab 314.3 with quinine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uin
Titlecrystal structure of quinine-dependent Fab 314.3 with quinine
Components(FAB 314.3) x 2
KeywordsIMMUNE SYSTEM / QUININE-DEPENDENT / MOUSE MAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Quinine
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhu, J. / Zhu, J. / Bougie, D.W. / Aster, R.H. / Springer, T.A.
CitationJournal: Blood / Year: 2015
Title: Structural Basis for Quinine-Dependent Antibody Binding to Platelet Integrin Alphaiib Beta3
Authors: Zhu, J. / Zhu, J. / Bougie, D.W. / Aster, R.H. / Springer, T.A.
History
DepositionMar 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Apr 19, 2017Group: Data collection
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: FAB 314.3
L: FAB 314.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1723
Polymers47,8482
Non-polymers3241
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-21.6 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.180, 55.460, 72.160
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody FAB 314.3


Mass: 24257.135 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 1-225 / Source method: isolated from a natural source / Details: ASCITES FLUID / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody FAB 314.3


Mass: 23590.900 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 1-214 / Source method: isolated from a natural source / Details: ASCITES FLUID / Source: (natural) MUS MUSCULUS (house mouse)
#3: Chemical ChemComp-QI9 / Quinine / (3alpha,8alpha,9R)-6'-methoxycinchonan-9-ol / Quinine


Mass: 324.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N2O2 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.24 Å3/Da / Density % sol: 45.04 % / Description: NONE
Crystal growpH: 7.5 / Details: 25% PEG 1500, PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2012 / Details: DOUBLE MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14747 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.11 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.5 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UIK

4uik


Resolution: 2.5→43.771 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 1006 6.8 %
Rwork0.203 --
obs0.2065 14737 99.36 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 24 90 3446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043449
X-RAY DIFFRACTIONf_angle_d0.9174690
X-RAY DIFFRACTIONf_dihedral_angle_d16.3441234
X-RAY DIFFRACTIONf_chiral_restr0.032527
X-RAY DIFFRACTIONf_plane_restr0.007595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.6320.31891520.28321881X-RAY DIFFRACTION97
2.632-2.79680.3311440.27411957X-RAY DIFFRACTION100
2.7968-3.01270.32021260.24731995X-RAY DIFFRACTION100
3.0127-3.31580.27711290.23371950X-RAY DIFFRACTION100
3.3158-3.79540.26471570.20031954X-RAY DIFFRACTION100
3.7954-4.78090.20371440.15331980X-RAY DIFFRACTION99
4.7809-43.77720.19481540.15292014X-RAY DIFFRACTION99
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)
11.35010.24081.32061.2973-0.1247.5509-0.02930.0641-0.0154-0.02160.04760.01010.00380.2237-0.05770.15170.0320.00830.11250.01140.2586.8127-15.2622-42.475
28.87710.237-2.39753.6325-0.89984.33870.0461-0.5735-0.18170.2080.0550.2582-0.0483-0.0621-0.05550.190.002-0.04070.180.00880.1787-11.4136-21.4221-11.2909
36.82821.6661-3.07381.3877-1.46814.5259-0.0483-0.1214-0.1841-0.04010.02050.03280.0608-0.130.02530.16960.0088-0.03040.1445-0.02960.2374-13.3079-6.0389-45.6169
45.4028-0.20213.82261.1507-0.18864.9378-0.3275-0.54220.48290.18920.0545-0.0313-0.323-0.0180.22710.24170.0291-0.0070.2983-0.07060.2865-16.5443-5.9664-9.7318
50.27420.0616-0.17970.0161-0.04340.122-0.066-0.0075-0.0682-0.0996-0.0063-0.09610.0452-0.0288-0.12220.31610.16170.07910.49110.13390.2624.807-6.8191-54.579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN H AND RESSEQ 1:121
2X-RAY DIFFRACTION2CHAIN H AND RESSEQ 122:222
3X-RAY DIFFRACTION3CHAIN L AND RESSEQ 1:108
4X-RAY DIFFRACTION4CHAIN L AND RESSEQ 109:212
5X-RAY DIFFRACTION5CHAIN H AND RESSEQ 1226:1226

+
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