[English] 日本語
Yorodumi
- PDB-4ya8: structure of plasmepsin II from Plasmodium Falciparum complexed w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ya8
Titlestructure of plasmepsin II from Plasmodium Falciparum complexed with inhibitor PG394
ComponentsPlasmepsin-2
KeywordsHYDROLASE / plasmepsin II / malaria / inhibitor
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
Chem-49W / Plasmepsin II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.301 Å
AuthorsRecacha, R. / Leitans, J. / Tars, K. / Jaudzems, K.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structures of plasmepsin II from Plasmodium falciparum in complex with two hydroxyethylamine-based inhibitors.
Authors: Recacha, R. / Leitans, J. / Akopjana, I. / Aprupe, L. / Trapencieris, P. / Jaudzems, K. / Jirgensons, A. / Tars, K.
#1: 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.
#2: Journal: 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
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plasmepsin-2
B: Plasmepsin-2
C: Plasmepsin-2
D: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,35411
Polymers147,6384
Non-polymers2,7157
Water543
1
A: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5192
Polymers36,9101
Non-polymers6101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6123
Polymers36,9101
Non-polymers7022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7044
Polymers36,9101
Non-polymers7943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Plasmepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5192
Polymers36,9101
Non-polymers6101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)177.770, 177.770, 177.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid A
31chain C and segid A
41chain D and segid A

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid AB0
311chain C and segid AC0
411chain D and segid AD0

-
Components

#1: Protein
Plasmepsin-2 / / Aspartic hemoglobinase II / PFAPD


Mass: 36909.617 Da / Num. of mol.: 4 / Mutation: M205S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli) / References: UniProt: P46925, plasmepsin II
#2: Chemical
ChemComp-49W / N'-[(2S,3S)-3-hydroxy-1-phenyl-4-{[2-(pyridin-2-yl)propan-2-yl]amino}butan-2-yl]-N,N-dipropyl-5-(pyridin-1(2H)-yl)benzene-1,3-dicarboxamide


Mass: 609.801 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H47N5O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M sodium citrate, 80 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.301→177.77 Å / Num. all: 27601 / Num. obs: 27601 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rpim(I) all: 0.068 / Rrim(I) all: 0.136 / Rsym value: 0.117 / Net I/av σ(I): 5.011 / Net I/σ(I): 7.5 / Num. measured all: 99396
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.3-3.483.60.6881.11440340530.4090.6881.899.1
3.48-3.693.60.4261.71370638460.250.4262.898.9
3.69-3.943.60.2861.61290236070.170.2864.198.9
3.94-4.263.60.1684.51203933430.0980.1686.498.1
4.26-4.673.60.1017.21109630710.0590.1019.497.8
4.67-5.223.60.0858.21007427650.0480.0851196.9
5.22-6.023.60.16.9877224100.0560.11196.4
6.02-7.383.70.0867.7753720450.0480.08612.794.8
7.38-10.443.70.03715.4575615720.0210.03716.294.2
10.44-59.2573.50.03511.231118890.0210.03518.492.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJU

2bju


Resolution: 3.301→56.216 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 1408 5.11 %
Rwork0.1881 26138 -
obs0.1893 27546 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.13 Å2 / Biso mean: 84.6093 Å2 / Biso min: 36.38 Å2
Refinement stepCycle: final / Resolution: 3.301→56.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10414 0 198 3 10615
Biso mean--82.15 50.53 -
Num. residues----1315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310936
X-RAY DIFFRACTIONf_angle_d0.80114879
X-RAY DIFFRACTIONf_chiral_restr0.0321651
X-RAY DIFFRACTIONf_plane_restr0.0041900
X-RAY DIFFRACTIONf_dihedral_angle_d11.4213872
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6276X-RAY DIFFRACTION7.273TORSIONAL
12B6276X-RAY DIFFRACTION7.273TORSIONAL
13C6276X-RAY DIFFRACTION7.273TORSIONAL
14D6276X-RAY DIFFRACTION7.273TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3005-3.41850.31321480.27882652280099
3.4185-3.55530.29611520.25562630278299
3.5553-3.71710.2541470.24262602274998
3.7171-3.9130.25371600.22762618277898
3.913-4.15810.25451490.19782604275398
4.1581-4.47910.17341280.16112623275197
4.4791-4.92960.16631350.14642636277197
4.9296-5.64230.18651150.16422603271896
5.6423-7.10650.22071260.19322609273595
7.1065-56.22390.17051480.1682561270992
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.4089-5.15421.03828.19655.40727.8132-0.1508-0.46280.0010.11220.5997-0.8570.5299-0.0156-0.37690.7721-0.12720.1450.82930.03590.7814-49.1721-15.5242-19.3312
24.3824-0.08870.57054.48961.19922.33620.2169-0.07580.2499-0.0573-0.14360.2339-0.2828-0.0194-0.11850.6358-0.13620.07480.68380.1430.4893-63.1779-6.6061-19.1468
37.5015-3.65963.05327.6371-4.5099.2032-0.36610.3191-0.0667-0.16020.04-1.05010.2523-0.32740.27380.7634-0.1850.17610.70830.12360.5644-48.3705-16.1862-29.8171
44.5910.19430.38812.6033-1.48840.7995-0.00140.3544-0.2863-0.36080.0757-0.12720.4024-0.0156-0.05310.8457-0.01830.10540.5908-0.0410.5587-61.0015-34.0579-29.1844
53.86660.4414-2.53255.2911-3.78658.251-0.2672-0.77610.17950.10140.10710.60860.34290.32510.00970.8023-0.07990.12960.609-0.0250.9434-58.8016-42.5605-15.9219
61.95020.6819-1.43475.4546-3.62345.22580.13850.2134-0.0202-0.3258-0.1867-0.07020.16460.47310.08180.7078-0.10960.10310.64570.01180.5422-54.2611-31.8726-22.4595
74.8602-3.72390.27933.8229-0.58193.78780.2981-0.27910.03070.0559-0.14150.72240.8041-0.7424-0.17570.7908-0.465-0.04771.08890.0430.7516-96.7722-34.4888-19.5763
82.2388-0.5394-0.02574.5257-1.46572.27470.03780.2506-0.252-0.37020.05060.41220.3038-0.4874-0.09090.679-0.2336-0.08160.80090.00220.5733-91.0442-33.8095-24.2096
95.25320.8449-0.20868.33395.15333.39810.43121.02390.90640.32830.0669-0.32430.0892-0.7093-0.47540.7111-0.1009-0.05750.82590.26780.6916-86.3332-8.8538-25.5182
104.41082.5793.26253.34790.82576.0310.41380.42140.2116-0.5752-0.00260.0727-0.00930.3949-0.420.93070.05740.32220.7169-0.14040.9328-90.948-2.2852-12.0896
112.88911.42680.23894.56642.33444.45620.02880.1490.466-0.3425-0.03230.56480.0035-0.5549-0.01480.622-0.1562-0.0720.84250.19550.8005-95.5817-14.2999-25.0506
122.52670.1911-0.51953.0253-0.01434.2542-0.1488-0.1026-0.30160.07290.07410.21630.3177-0.29360.08730.50860.03290.01060.60470.14660.6987-64.25894.547-53.0516
132.1211.538-1.01395.6138-1.50893.5222-0.0002-0.23960.03270.6023-0.0680.6982-0.4333-0.23210.03940.62910.25150.06410.9436-0.09450.676-70.814426.5572-48.5201
142.76093.6887-1.81555.9651-0.64593.9044-0.0331-0.455-0.47220.9036-0.0439-0.07480.09180.51020.17720.93790.1839-0.12160.5769-0.04550.8165-58.360937.9732-48.2717
156.73292.2387-2.33384.2203-1.67813.02970.2379-0.70690.03450.2907-0.2140.464-0.8173-0.2557-0.19070.73170.2169-0.00170.78-0.00160.6258-65.764227.0152-45.8151
167.28486.8321-1.64167.0308-2.65432.47550.4815-0.13551.1443-1.2537-0.3331.01170.1774-0.36820.39590.86150.10920.09510.8968-0.10170.7212-33.6698-29.8648-1.9383
174.32641.3085-1.89116.4478-0.19725.613-0.08050.019-0.30260.14760.0502-0.18950.3326-0.08860.00780.6160.14640.16070.63010.00620.6377-32.4389-37.791112.3165
182.10111.2817-1.63294.3943-1.50692.81850.25850.43470.4626-2.0554-0.1605-1.49350.319-0.2474-0.03021.14650.24450.40680.8367-0.0580.7802-22.9789-30.8312-4.4679
193.0306-1.4364-1.72846.17722.10725.29290.3033-0.44490.0291-0.6249-0.2465-0.4328-0.41990.54320.08360.67550.03140.25860.61990.10380.7794-19.9738-12.08186.1602
202.3450.1650.98712.279-3.03214.92290.18560.18370.49640.96290.6986-0.17450.1304-0.7542-0.62390.90170.18810.19980.7202-0.00260.8587-37.5709-0.33946.0351
211.9463-1.3078-2.44732.25621.68533.10160.95471.62770.306-1.1955-0.6887-0.4151-1.2825-0.7918-0.13281.14350.36590.25171.09890.08610.8081-21.7592-8.3982-1.67
222.4495-3.23612.45388.1955-2.59292.61431.4617-0.08620.5553-1.8257-0.87741.34141.1708-0.6468-0.1711.08410.0647-0.0740.71350.0261.0827-41.3757-7.0391.3596
233.3405-0.8999-1.8724.80973.62876.7999-0.05050.1837-0.6808-0.9048-0.0275-0.7641-0.10920.56290.03580.73390.05970.25480.5108-0.01850.664-21.8931-18.57411.1696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 138 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 177 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 231 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 232 through 264 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 265 through 329 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 43 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 201 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 202 through 231 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 232 through 256 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 257 through 329 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 157 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 158 through 231 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 232 through 264 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 265 through 329 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 22 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 23 through 138 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 139 through 177 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 178 through 231 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 232 through 256 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 257 through 273 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 274 through 291 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 292 through 329 )D0

+
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