[English] 日本語
Yorodumi
- PDB-5muh: Crystal structure of an amyloidogenic light chain dimer H7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5muh
TitleCrystal structure of an amyloidogenic light chain dimer H7
Componentslight chain dimer
KeywordsIMMUNE SYSTEM / light chain dimer / light chain amyloidosis / immunoglobulin fold / protein aggregation
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsOberti, L. / Rognoni, P. / Russo, R. / Maritan, M. / Bacarizo, J. / Bolognesi, M. / Ricagno, S.
CitationJournal: Sci Rep / Year: 2017
Title: Concurrent structural and biophysical traits link with immunoglobulin light chains amyloid propensity.
Authors: Oberti, L. / Rognoni, P. / Barbiroli, A. / Lavatelli, F. / Russo, R. / Maritan, M. / Palladini, G. / Bolognesi, M. / Merlini, G. / Ricagno, S.
History
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: light chain dimer
B: light chain dimer


Theoretical massNumber of molelcules
Total (without water)44,6952
Polymers44,6952
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-16 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.010, 72.820, 73.720
Angle α, β, γ (deg.)90.00, 121.19, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody light chain dimer


Mass: 22347.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH7.5, 10% 2-propanol, 20% w/v PEG 4K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.65→50.99 Å / Num. obs: 13069 / % possible obs: 97 % / Redundancy: 3.5 % / Biso Wilson estimate: 65.84 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.6
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1879 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M6I

5m6i


Resolution: 2.65→55.45 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.858 / SU R Cruickshank DPI: 0.72 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.631 / SU Rfree Blow DPI: 0.321 / SU Rfree Cruickshank DPI: 0.332
RfactorNum. reflection% reflectionSelection details
Rfree0.266 635 4.92 %RANDOM
Rwork0.205 ---
obs0.208 12897 97.2 %-
all-13069 --
Displacement parametersBiso mean: 105.61 Å2
Baniso -1Baniso -2Baniso -3
1--5.6974 Å20 Å239.3581 Å2
2--37.6832 Å20 Å2
3----31.9858 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: 1 / Resolution: 2.65→55.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 0 26 2812
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092860HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.23905HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d903SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes408HARMONIC5
X-RAY DIFFRACTIONt_it2860HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion20.45
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion401SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3066SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.9 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 140 4.81 %
Rwork0.2241 2772 -
all0.2276 2912 -
obs--92.92 %
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)
13.69620.59380.95641.5079-0.93021.87110.1081-0.5541-0.0120.7522-0.10060.12960.1081-0.1371-0.00750.04850.07480.0037-0.2208-0.127-0.004-15.124419.874311.7154
25.1190.83022.53582.00970.81544.5790.158-0.5294-0.64440.25440.1516-0.19420.2389-0.1541-0.30950.09330.082-0.0756-0.3647-0.05910.0399-14.36073.34739.4529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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