[English] 日本語
Yorodumi
- PDB-3s5m: Crystal structures of falcilysin, a M16 metalloprotease from the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s5m
TitleCrystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum
ComponentsFalcilysin
KeywordsHYDROLASE / M16 metalloprotease / peptidase
Function / homology
Function and homology information


hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / metalloendopeptidase activity / protein processing / metal ion binding
Similarity search - Function
: / Peptidase M16C associated / Peptidase M16C associated / PreP C-terminal domain / 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
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.55 Å
AuthorsMorgunova, E. / Ponpuak, M. / Istvan, E. / Popov, A. / Goldberg, D. / Eneqvist, T.
CitationJournal: To be Published
Title: Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum
Authors: Morgunova, E. / Ponpuak, M. / Istvan, E. / Popov, A. / Goldberg, D. / Eneqvist, T.
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
A: Falcilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,1644
Polymers139,0501
Non-polymers1143
Water19,8711103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.320, 106.700, 128.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Falcilysin


Mass: 139050.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: HB3 / Gene: flN, PF13_0322 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76NL8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1103 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 11% PEG6000, 10% PEG400, 0.1M ADA, 20 mM Mg acetate, 20 mM Zn acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2010 / Details: bent cylindrical mirror
RadiationMonochromator: single crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.51→29.2 Å / Num. all: 866049 / Num. obs: 866049 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.6
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / Num. unique all: 24464 / % possible all: 83.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.autoMR:1.6_489)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIR
Starting model: 2FGE

2fge


Resolution: 1.55→29.2 Å / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.94 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 7163 2 %random
Rwork0.1789 ---
all0.19 ---
obs0.1796 358227 98.87 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.606 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.7528 Å2-0 Å20 Å2
2---0.3162 Å2-0 Å2
3---1.0689 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8980 0 3 1103 10086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149390
X-RAY DIFFRACTIONf_angle_d1.61612713
X-RAY DIFFRACTIONf_dihedral_angle_d14.1213633
X-RAY DIFFRACTIONf_chiral_restr0.1921397
X-RAY DIFFRACTIONf_plane_restr0.0081635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5499-1.60530.27696970.248534211X-RAY DIFFRACTION96
1.6053-1.66960.27827130.226235087X-RAY DIFFRACTION99
1.6696-1.74560.22867130.200735110X-RAY DIFFRACTION99
1.7456-1.83760.25567250.192335205X-RAY DIFFRACTION99
1.8376-1.95270.23897140.221935169X-RAY DIFFRACTION99
1.9527-2.10340.22637170.178835155X-RAY DIFFRACTION99
2.1034-2.3150.22567170.18234886X-RAY DIFFRACTION98
2.315-2.64980.21227190.160835287X-RAY DIFFRACTION99
2.6498-3.33780.19877290.16935484X-RAY DIFFRACTION100
3.3378-29.53240.18997190.165435470X-RAY DIFFRACTION100

+
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