[English] 日本語
Yorodumi
- PDB-4kiv: RECOMBINANT KRINGLE IV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kiv
TitleRECOMBINANT KRINGLE IV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A)
ComponentsAPOLIPOPROTEIN
KeywordsLYSINE BINDING SITE / SITE MUTATION
Function / homology
Function and homology information


plasma lipoprotein particle / LDL remodeling / blood circulation / endopeptidase inhibitor activity / lipid transport / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / apolipoprotein binding / lipid metabolic process / heparin binding ...plasma lipoprotein particle / LDL remodeling / blood circulation / endopeptidase inhibitor activity / lipid transport / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / apolipoprotein binding / lipid metabolic process / heparin binding / serine-type endopeptidase activity / proteolysis / 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 ...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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMochalkin, I. / Tulinsky, A. / Scanu, A.
CitationJournal: Biochemistry / Year: 1999
Title: Recombinant kringle IV-10 modules of human apolipoprotein(a): structure, ligand binding modes, and biological relevance.
Authors: Mochalkin, I. / Cheng, B. / Klezovitch, O. / Scanu, A.M. / Tulinsky, A.
History
DepositionAug 26, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APOLIPOPROTEIN


Theoretical massNumber of molelcules
Total (without water)9,1701
Polymers9,1701
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.300, 45.820, 56.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein APOLIPOPROTEIN


Mass: 9170.088 Da / Num. of mol.: 1 / Fragment: KRINGLE IV-10 / Mutation: W72R
Source method: isolated from a genetically manipulated source
Details: KIV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08519
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Compound detailsN-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRINGULAR PARTS ARE DISORDERED. SIDE CHAIN FOR ...N-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRINGULAR PARTS ARE DISORDERED. SIDE CHAIN FOR RESIDUE GLN0 IS MISSING. THE P30 RESIDUE IS IN CIS CONFORMATION.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.56 Å3/Da / Density % sol: 22 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 %PEG80001reservoir
30.1 Msodium cacodylate1reservoir
40.1 M1reservoirLi2SO4

-
Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MSC-YALE MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→24.3 Å / Num. obs: 6494 / % possible obs: 64 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.2
Reflection shellResolution: 2.2→2.5 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 2 / % possible all: 45
Reflection
*PLUS
Num. obs: 2241 / Num. measured all: 6494
Reflection shell
*PLUS
% possible obs: 45 % / Rmerge(I) obs: 0.089

-
Processing

Software
NameVersionClassification
RIGAKUR-AXISdata collection
RIGAKUR-AXISdata reduction
AMoREphasing
PROFFTrefinement
R-AXIS(RIGAKU)data reduction
R-AXIS(RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→7 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.162 --
obs-2114 44 %
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 0 41 673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0461.5
X-RAY DIFFRACTIONp_mcangle_it1.6452
X-RAY DIFFRACTIONp_scbond_it1.7482.3
X-RAY DIFFRACTIONp_scangle_it2.4562.5
X-RAY DIFFRACTIONp_plane_restr0.0280.03
X-RAY DIFFRACTIONp_chiral_restr0.130.12
X-RAY DIFFRACTIONp_singtor_nbd0.220.6
X-RAY DIFFRACTIONp_multtor_nbd0.280.6
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.290.6
X-RAY DIFFRACTIONp_planar_tor43
X-RAY DIFFRACTIONp_staggered_tor1915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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