[English] 日本語
Yorodumi
- PDB-1pfz: PROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pfz
TitlePROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM
ComponentsPROPLASMEPSIN II
KeywordsASPARTIC PROTEASE ZYMOGEN / ASPARTIC PROTEINASE ZYMOGEN / HEMOGLOBINASE / MALARIA / HYDROLASE / ASPARTYL PROTEASE / GLYCOPROTEIN
Function / homology
Function and homology information


cytostome / plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / proteolysis
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
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBernstein, N.K. / Cherney, M.M. / Loetscher, H. / Ridley, R.G. / James, M.N.G.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from plasmodium falciparum.
Authors: Bernstein, N.K. / Cherney, M.M. / Loetscher, H. / Ridley, R.G. / James, M.N.
#1: Journal: FEBS Lett. / Year: 1994
Title: High Level Expression and Characterisation of Plasmepsin II, an Aspartic Proteinase from Plasmodium Falciparum
Authors: Hill, J. / Tyas, L. / Phylip, L.H. / Kay, J. / Dunn, B.M. / Berry, C.
History
DepositionJul 7, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROPLASMEPSIN II
B: PROPLASMEPSIN II
C: PROPLASMEPSIN II
D: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,48610
Polymers170,9334
Non-polymers5536
Water13,169731
1
A: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0104
Polymers42,7331
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROPLASMEPSIN II


Theoretical massNumber of molelcules
Total (without water)42,7331
Polymers42,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8252
Polymers42,7331
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9183
Polymers42,7331
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: PROPLASMEPSIN II
D: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5593
Polymers85,4672
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-16 kcal/mol
Surface area31330 Å2
MethodPISA
6
A: PROPLASMEPSIN II
C: PROPLASMEPSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9277
Polymers85,4672
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-19 kcal/mol
Surface area31580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.007, 133.223, 114.234
Angle α, β, γ (deg.)90.00, 98.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999952, 0.002348, 0.009486), (0.002185, -0.999849, 0.017241), (0.009525, -0.01722, -0.999806)-26.9129, 31.2322, 146.6722
2given(-0.999873, -0.009973, -0.012427), (-0.009592, 0.999495, -0.030297), (0.012723, -0.030174, -0.999464)8.1204, 3.9222, 158.36391
3given(-0.999616, -0.027342, -0.004556), (0.027681, -0.976002, -0.215994), (0.001459, -0.216037, 0.976384)32.1287, 45.2125, 17.1313

-
Components

#1: Protein
PROPLASMEPSIN II


Mass: 42733.336 Da / Num. of mol.: 4
Mutation: 76 RESIDUES AT THE N-TERMINUS OF THE PROSEGMENT (1P - 76P) HAVE BEEN TRUNCATED, 3 RESIDUES (GLY-ARG-GLY) HAVE BEEN ADDED AT THE N-TERMINUS AS AN ARTIFACT OF THE EXPRESSION SYSTEM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Cell line: BL21 / Organelle: DIGESTIVE VACUOLE / Plasmid: PBLUESCRIPT KS+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P46925, plasmepsin II
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNOMENCLATURE: THE PROSEGMENT RESIDUES HAVE INSERTION CODE P (78/79 P - 118/124 P). NUMBERING FOR ...NOMENCLATURE: THE PROSEGMENT RESIDUES HAVE INSERTION CODE P (78/79 P - 118/124 P). NUMBERING FOR THE MATURE SEGMENT CORRESPONDS TO P. FALCIPARUM PLASMEPSIN II, PDB ENTRY 1SME.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 105 K / Method: vapor diffusion, sitting drop
Details: 2 microlitter of protein splution was mixed with 7 microlitter of reservoir solution
PH range low: 8 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127 mg/mlprotein1drop
225 %PEG40001reservoir
30.18 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoir
50.1 %beta-octylglucoside1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 114943 / % possible obs: 96.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3 / % possible all: 91.5
Reflection shell
*PLUS
% possible obs: 91.5 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3refinement
CNS0.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2505951.19 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED DATA CUTOFF HIGH (ABS(F)) : 2505951.19 DATA CUTOFF LOW (ABS(F)) : 0.000000
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2699 2.1 %RANDOM
Rwork0.214 ---
obs0.214 125751 96.1 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å2-0.11 Å2
2---5.19 Å20 Å2
3---2.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11648 0 36 731 12415
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_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 419 2.1 %
Rwork0.276 19202 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMGLR.TOP
X-RAY DIFFRACTION3GLR.PARAM
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
LS refinement shell
*PLUS
Rfactor obs: 0.276

+
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://pdbjlvh1.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