[English] 日本語
Yorodumi
- PDB-6rx7: Structure of the KIV type 2 (KIV-2) domain of lipoprotein (a) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rx7
TitleStructure of the KIV type 2 (KIV-2) domain of lipoprotein (a)
ComponentsApolipoprotein(a)
KeywordsLIPID TRANSPORT / Lipoprotein (a) / kringle IV type 2 / KIV-2 / Lp(a).
Function / homology
Function and homology information


plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / lipid metabolic process / heparin binding ...plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / lipid metabolic process / heparin binding / endopeptidase activity / signaling receptor binding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region
Similarity search - Function
Plasminogen Kringle 4 / Plasminogen Kringle 4 / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold ...Plasminogen Kringle 4 / Plasminogen Kringle 4 / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSantonastaso, A. / Maggi, M. / Scotti, C.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione CARIPLO42657763 (2013-0380) Italy
CitationJournal: J.Lipid Res. / Year: 2020
Title: High resolution structure of human apolipoprotein (a) kringle IV type 2: beyond the lysine binding site.
Authors: Santonastaso, A. / Maggi, M. / De Jonge, H. / Scotti, C.
History
DepositionJun 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 24, 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apolipoprotein(a)
B: Apolipoprotein(a)
C: Apolipoprotein(a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,68613
Polymers37,7573
Non-polymers92910
Water4,017223
1
A: Apolipoprotein(a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9545
Polymers12,5861
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apolipoprotein(a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0546
Polymers12,5861
Non-polymers4685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Apolipoprotein(a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6782
Polymers12,5861
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.246, 42.839, 61.175
Angle α, β, γ (deg.)90.000, 110.230, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Apolipoprotein(a) / Lp(a)


Mass: 12585.704 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LPA / Plasmid: pET45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P08519, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG400 1% (v/v) Ammonium sulfate 2 M HEPES 0.1 M

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.424→56.413 Å / Num. obs: 38419 / % possible obs: 82.9 % / Redundancy: 3 % / Biso Wilson estimate: 17.42 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.5
Reflection shellResolution: 1.424→1.541 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1922 / CC1/2: 0.556 / % possible all: 45.6

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSVERSION Jan 26, 2018 BUILT=20180126data reduction
Aimless0.7.1data scaling
PHASER1.11.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KIV, 3KIV, 4BVW

1kiv

3kiv

4bvw


Resolution: 1.63→34.92 Å / Cross valid method: THROUGHOUT / Phase error: 28.87
RfactorNum. reflection% reflection
Rfree0.269 1999 5.43 %
Rwork0.232 --
obs0.234 36781 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.42 Å2 / Biso mean: 22.8234 Å2 / Biso min: 7.42 Å2
Refinement stepCycle: final / Resolution: 1.63→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 58 223 2344
Biso mean--40.75 29.3 -
Num. residues----263

+
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