[English] 日本語
Yorodumi
- PDB-7vpe: Falcilysin in complex with A1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vpe
TitleFalcilysin in complex with A1
ComponentsFalcilysin
KeywordsPROTEIN BINDING / Falcilysin / A1 / protease-inhibitor complex
Function / homology
Function and homology information


hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / protein processing / metalloendopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M16C associated / Peptidase M16C associated / Peptidase M16C associated / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like
Similarity search - Domain/homology
Chem-7TU / ACETATE ION / Falcilysin
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLin, J.Q. / El Sahili, A. / Lescar, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: To Be Published
Title: Title is not available yet as we are preparing the manuscript. Will update again once the paper is out.
Authors: Lin, J.Q. / Lescar, J.
History
DepositionOct 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Falcilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,94611
Polymers135,0391
Non-polymers90710
Water19,0421057
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-34 kcal/mol
Surface area43380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.663, 106.157, 126.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Falcilysin


Mass: 135039.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: FLN / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U7N7

-
Non-polymers , 6 types, 1067 molecules

#2: Chemical ChemComp-7TU / (4S,5S)-1-[[3-[[(4S,5S)-4,5-diphenyl-4,5-dihydroimidazol-1-yl]methyl]phenyl]methyl]-4,5-diphenyl-4,5-dihydroimidazole


Mass: 546.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H34N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1057 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Morpheus G1 (0.1 M carboxylic acids, 0.1 M buffer system 1 pH 6.5, 10% w/v PEG 20,000, 20% v/v PEG 550mme)

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1.24 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 157897 / % possible obs: 99.57 % / Redundancy: 2 % / Biso Wilson estimate: 25.69 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.02663 / Rpim(I) all: 0.02663 / Rrim(I) all: 0.03765 / Net I/σ(I): 13.79
Reflection shellResolution: 1.624→1.682 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2978 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 15104 / CC1/2: 0.786 / CC star: 0.938 / Rpim(I) all: 0.2978 / Rrim(I) all: 0.4212 / % possible all: 95.96

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S5H

3s5h


Resolution: 1.62→46.92 Å / SU ML: 0.2386 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 2000 1.27 %
Rwork0.1796 155876 -
obs0.1798 157876 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 1.62→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8847 0 54 1057 9958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00659081
X-RAY DIFFRACTIONf_angle_d0.865712230
X-RAY DIFFRACTIONf_chiral_restr0.05811334
X-RAY DIFFRACTIONf_plane_restr0.00481560
X-RAY DIFFRACTIONf_dihedral_angle_d17.15673474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.40221340.34510476X-RAY DIFFRACTION94.73
1.66-1.710.30941420.276311024X-RAY DIFFRACTION99.53
1.71-1.760.25591420.232411062X-RAY DIFFRACTION100
1.76-1.820.23941420.200811063X-RAY DIFFRACTION100
1.82-1.880.23611420.190511109X-RAY DIFFRACTION99.98
1.88-1.960.20671430.183211114X-RAY DIFFRACTION99.99
1.96-2.050.22381420.18611121X-RAY DIFFRACTION100
2.05-2.150.21041440.18211147X-RAY DIFFRACTION99.98
2.15-2.290.19131430.179911145X-RAY DIFFRACTION99.98
2.29-2.470.18961430.182611192X-RAY DIFFRACTION99.99
2.47-2.710.18961440.182111182X-RAY DIFFRACTION99.98
2.71-3.110.18671440.185911233X-RAY DIFFRACTION100
3.11-3.910.18491460.16511340X-RAY DIFFRACTION99.99
3.91-46.920.1731490.161211668X-RAY DIFFRACTION99.82

+
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