[English] 日本語
Yorodumi
- PDB-3qvi: Crystal structure of KNI-10395 bound histo-aspartic protease (HAP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qvi
TitleCrystal structure of KNI-10395 bound histo-aspartic protease (HAP) from Plasmodium falciparum
ComponentsHisto-aspartic protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Histo-aspartic protease / HAP / Plasmepsin / Aspartic protease / Malaria / KNI / KNI-10395 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / 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 domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
KNI-10395 / ACETATE ION / Chem-K95 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Plasmepsin III
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBhaumik, P. / Gustchina, A. / Wlodawer, A.
CitationJournal: Biochemistry / Year: 2011
Title: Structural insights into the activation and inhibition of histo-aspartic protease from Plasmodium falciparum.
Authors: Bhaumik, P. / Xiao, H. / Hidaka, K. / Gustchina, A. / Kiso, Y. / Yada, R.Y. / Wlodawer, A.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 4, 2013Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histo-aspartic protease
B: Histo-aspartic protease
C: Histo-aspartic protease
D: Histo-aspartic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,91726
Polymers207,0204
Non-polymers3,89722
Water9,152508
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histo-aspartic protease
B: Histo-aspartic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,28312
Polymers103,5102
Non-polymers1,77310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-44 kcal/mol
Surface area26560 Å2
MethodPISA
3
C: Histo-aspartic protease
D: Histo-aspartic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,63414
Polymers103,5102
Non-polymers2,12412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-40 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.430, 90.510, 192.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A0 - 73
2114B0 - 73
1214A81 - 155
2214B81 - 155
1314A164 - 228
2314B164 - 228
1414A255 - 278
2414B255 - 278
1514A281 - 327
2514B281 - 327
1124C0 - 73
2124D0 - 73
1224C81 - 155
2224D81 - 155
1324C164 - 228
2324D164 - 228
1424C255 - 278
2424D255 - 278
1524C281 - 327
2524D281 - 327

NCS ensembles :
ID
1
2

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Histo-aspartic protease / HAP protein / Putative aspartic proteinase


Mass: 51754.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: hap / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) pLysS / References: UniProt: Q9Y006

-
Non-polymers , 7 types, 530 molecules

#2: Chemical ChemComp-K95 / (4R)-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-3-[(2S,3S)-2-hydroxy-3-{[S-methyl-N-(phenylacetyl)-L-cysteinyl]amino}-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide / KNI-10395


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 704.898 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H44N4O6S2 / References: KNI-10395
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Triethylene glycol dimethyl ether


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 508 / 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: 1.86 Å3/Da / Density % sol: 33.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% (v/v) PEG 200, 0.1M Sodium Chloride, 0.1M Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 79116 / Num. obs: 79116 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.209 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.1902 / Mean I/σ(I) obs: 1.05 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.72 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.907 / SU B: 20.656 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25187 2712 5 %RANDOM
Rwork0.17503 ---
obs0.17882 51509 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.922 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10393 0 255 508 11156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02211063
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.931.98215021
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36651351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11925.644489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.063151867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7921512
X-RAY DIFFRACTIONr_chiral_restr0.1490.21667
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218318
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7691.56607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.478210804
X-RAY DIFFRACTIONr_scbond_it2.30134456
X-RAY DIFFRACTIONr_scangle_it3.8084.54192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 198 -
Rwork0.245 3750 -
obs--100 %
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)
12.16060.27480.04771.28140.27032.4821-0.0438-0.1140.23370.10480.02360.0498-0.1973-0.35510.02030.05950.04530.02930.1718-0.02050.06581.349-7.1617.825
23.2871-1.2961-0.27831.6583-0.13462.2603-0.00140.3040.26980.0473-0.0441-0.1499-0.06230.15270.04550.1128-0.0398-0.00580.15460.03270.049717.428-12.281-11.003
31.6292-0.05360.50890.81150.04212.83850.00240.11290.1360.01320.0225-0.0693-0.22480.4158-0.02480.1007-0.0272-0.00390.20380.02550.068521.079-9.08-11.333
43.49361.55830.50621.11090.36880.172-0.20640.3040.4452-0.47570.10550.242-0.34860.02650.1011.1283-0.0845-0.22140.31690.1320.303829.95822.242-5.14
50.9688-0.40520.45572.88190.4062.2477-0.23110.1930.2378-0.43240.1120.011-0.82390.38490.11910.4849-0.1564-0.07540.26650.00350.168836.66611.7627.439
61.66580.64241.42011.23970.85252.5854-0.1520.09080.1102-0.17990.10710.0215-0.32720.2860.04490.1558-0.03-0.00780.1753-0.0130.054633.729-1.68412.722
72.2283-0.92310.20021.74360.74781.2699-0.02130.1173-0.1177-0.0651-0.03660.0655-0.1187-0.2460.0580.07290.0444-0.02050.29-0.0670.06062.58110.65740.709
84.48731.10620.23021.22360.52663.37610.0042-0.2281-0.21370.0102-0.0355-0.0362-0.1333-0.19370.03120.09110.02660.00840.17470.0180.040115.05513.1159.895
90.9094-0.56050.14131.2710.70292.0597-0.009-0.0865-0.0432-0.00350.0804-0.1259-0.0630.1315-0.07140.0966-0.00020.01210.2047-0.02320.070723.4229.60460.061
101.8422-0.387-0.22472.5124-0.67421.25770.0281-0.1536-0.04370.0790.00180.057-0.0484-0.1314-0.030.0185-0.0084-0.01690.14410.01630.058327.342-23.10652.999
111.72281.1417-0.12892.7847-0.11161.0302-0.07110.01820.0001-0.16510.0634-0.00860.0687-0.03440.00760.08170.0234-0.01550.1861-0.02950.026335.521-8.56835.948
120.9408-0.037-0.4511.4983-0.07280.99590.0138-0.06010.0725-0.02960.0336-0.0679-0.04690.0441-0.04740.06770.0002-0.01830.1698-0.02290.021233.6810.04336.45
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 149
2X-RAY DIFFRACTION2A150 - 245
3X-RAY DIFFRACTION3A246 - 327
4X-RAY DIFFRACTION4B0 - 95
5X-RAY DIFFRACTION5B96 - 237
6X-RAY DIFFRACTION6B238 - 327
7X-RAY DIFFRACTION7C0 - 149
8X-RAY DIFFRACTION8C150 - 230
9X-RAY DIFFRACTION9C231 - 327
10X-RAY DIFFRACTION10D0 - 148
11X-RAY DIFFRACTION11D149 - 235
12X-RAY DIFFRACTION12D236 - 327

+
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