[English] 日本語
Yorodumi
- PDB-1qs8: Crystal structure of the P. vivax aspartic proteinase plasmepsin ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qs8
TitleCrystal structure of the P. vivax aspartic proteinase plasmepsin complexed with the inhibitor pepstatin A
Components
  • PEPSTATIN A
  • PLASMEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PLASMEPSIN / ASPARTIC PROTEINASE / HAEMOGLOBINASE / MALARIA / PEPSTATIN A / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pepstatin / ACETATE ION / : / (malaria parasite P. vivax) hypothetical protein
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Streptomyces argenteolus subsp. toyonakensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsKhazanovich Bernstein, N. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural insights into the activation of P. vivax plasmepsin.
Authors: Bernstein, N.K. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N.
History
DepositionJun 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: PLASMEPSIN
B: PLASMEPSIN
C: PEPSTATIN A
D: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8086
Polymers75,6894
Non-polymers1182
Water2,774154
1
A: PLASMEPSIN
C: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9043
Polymers37,8452
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-12 kcal/mol
Surface area14320 Å2
MethodPISA
2
B: PLASMEPSIN
D: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9043
Polymers37,8452
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-10 kcal/mol
Surface area14170 Å2
MethodPISA
3
A: PLASMEPSIN
C: PEPSTATIN A
hetero molecules

B: PLASMEPSIN
D: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8086
Polymers75,6894
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
Buried area5480 Å2
ΔGint-47 kcal/mol
Surface area26130 Å2
MethodPISA
4
A: PLASMEPSIN
B: PLASMEPSIN
C: PEPSTATIN A
D: PEPSTATIN A
hetero molecules

A: PLASMEPSIN
B: PLASMEPSIN
C: PEPSTATIN A
D: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,61512
Polymers151,3798
Non-polymers2364
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)145.015, 145.015, 71.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein PLASMEPSIN


Mass: 37158.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Production host: Bacteria (eubacteria) / References: GenBank: AAC15792, UniProt: O60989*PLUS
#2: Protein/peptide PEPSTATIN A


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Streptomyces argenteolus subsp. toyonakensis (bacteria)
References: Pepstatin
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 3000, AMMONIUM SULFATE, ACETATE, AMYL ALCOHOL, BETA-OCTYL GLUCOSIDE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 %(v/v)PEG30001reservoir
20.2 Mammonium sulfate1reservoir
30.1 MNa acetate1reservoir
43 %(v/v)MPD1reservoir
50.15 %(w/v)beta-octylglucoside1reservoir

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.47→25 Å / Num. all: 27767 / Num. obs: 27347 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.4
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 130851
Reflection shell
*PLUS
% possible obs: 97.3 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2.5→25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2434582.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1353 5.1 %RANDOM
Rwork0.197 ---
obs0.197 26324 98.4 %-
all-26791 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.63 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å20 Å20 Å2
2--3.37 Å20 Å2
3----6.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 8 154 5472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.461.5
X-RAY DIFFRACTIONc_mcangle_it3.932
X-RAY DIFFRACTIONc_scbond_it3.812
X-RAY DIFFRACTIONc_scangle_it5.322.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 200 4.7 %
Rwork0.264 4081 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_PEPST_REP.PARAMPROTEIN_PEPST.TOP
X-RAY DIFFRACTION2WATER_REP.PARAACETATE.TOP
X-RAY DIFFRACTION3WATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

+
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