[English] 日本語
Yorodumi
- PDB-6dfk: Crystal structure of the 11S subunit of the Plasmodium falciparum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dfk
TitleCrystal structure of the 11S subunit of the Plasmodium falciparum proteasome, PA28
ComponentsSubunit of proteaseome activator complex,putative
KeywordsPROTEIN BINDING / 11S proteasome subunit / 11S regulatory particle / PA28 / REG / proteasome activator / hydrolase activator
Function / homology
Function and homology information


Ub-specific processing proteases / Orc1 removal from chromatin / UCH proteinases / positive regulation of endopeptidase activity / proteasome activator complex / regulation of G1/S transition of mitotic cell cycle / endopeptidase activator activity / regulation of proteasomal protein catabolic process / peptidase activity / nucleoplasm / cytoplasm
Proteasome activator PA28, C-terminal domain / Proteasome activator PA28 / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator pa28 beta subunit
Subunit of proteaseome activator complex,putative
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsXie, S.C. / Metcalfe, R.D. / Gillett, D.L. / Tilley, L. / Griffin, M.D.W.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia) Australia
Australian Research Council Australia
Global Health Innovative Technology Fund
GSK Tres Cantos Open Lab Foundation
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Subunit of proteaseome activator complex,putative
B: Subunit of proteaseome activator complex,putative
C: Subunit of proteaseome activator complex,putative
D: Subunit of proteaseome activator complex,putative
E: Subunit of proteaseome activator complex,putative
F: Subunit of proteaseome activator complex,putative
G: Subunit of proteaseome activator complex,putative
H: Subunit of proteaseome activator complex,putative
I: Subunit of proteaseome activator complex,putative
J: Subunit of proteaseome activator complex,putative
K: Subunit of proteaseome activator complex,putative
L: Subunit of proteaseome activator complex,putative
M: Subunit of proteaseome activator complex,putative
N: Subunit of proteaseome activator complex,putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,06574
Polymers465,30214
Non-polymers5,76460
Water0
1
A: Subunit of proteaseome activator complex,putative
B: Subunit of proteaseome activator complex,putative
C: Subunit of proteaseome activator complex,putative
D: Subunit of proteaseome activator complex,putative
E: Subunit of proteaseome activator complex,putative
F: Subunit of proteaseome activator complex,putative
G: Subunit of proteaseome activator complex,putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,53337
Polymers232,6517
Non-polymers2,88230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43800 Å2
ΔGint-640 kcal/mol
Surface area67770 Å2
MethodPISA
2
H: Subunit of proteaseome activator complex,putative
I: Subunit of proteaseome activator complex,putative
J: Subunit of proteaseome activator complex,putative
K: Subunit of proteaseome activator complex,putative
L: Subunit of proteaseome activator complex,putative
M: Subunit of proteaseome activator complex,putative
N: Subunit of proteaseome activator complex,putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,53337
Polymers232,6517
Non-polymers2,88230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44790 Å2
ΔGint-640 kcal/mol
Surface area67540 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)166.485, 166.485, 399.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein/peptide
Subunit of proteaseome activator complex,putative


Mass: 33235.824 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_0907700 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I374
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: SO4 / Sulfate

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20 mM HEPES, 2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→48.89 Å / Num. obs: 116975 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 60.6 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.131 / Rrim(I) all: 0.305 / Net I/σ(I): 7.5
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5711 / CC1/2: 0.513 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVO

1avo


Resolution: 3.1→48.89 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 22.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 3534 3.02 %Random; Thin shells
Rwork0.1817 ---
Obs0.183 116839 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26198 0 300 0 26498
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.00326942
f_angle_d0.63636381
f_dihedral_angle_d1.84616405
f_chiral_restr0.0453963
f_plane_restr0.0034545
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.1-3.21080.31742270.29911348
3.2108-3.33930.31085340.26211020
3.3393-3.49120.26711930.23711333
3.4912-3.67530.28693580.217311225
3.6753-3.90540.23994030.185911185
3.9054-4.20680.19024490.149711179
4.2068-4.62990.18112640.136611437
4.6299-5.29910.1923620.141311326
5.2991-6.67370.22133660.188811479
6.6737-48.89630.20813780.169511773
Refinement TLS params.

Method: refined / Refinement-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)
10.577-0.22610.18231.7646-0.33821.57250.1433-0.1079-0.13770.1671-0.028-0.04710.3541-0.0557-0.08930.5749-0.1187-0.03350.34020.05590.3769-69.24425.266316.7894
20.8044-0.63860.1012.94250.07791.29590.0473-0.0281-0.0859-0.088-0.01970.10950.1952-0.1856-0.06080.3818-0.1402-0.03530.37310.01610.278-72.398433.4304-4.7258
31.2078-0.4785-0.53811.76770.451.4733-0.0578-0.019-0.0345-0.06940.1104-0.07940.05440.1669-0.08310.3565-0.0835-0.06050.42720.0190.2811-62.432351.0072-15.8381
41.8457-0.2905-0.74961.63040.71872.4639-0.15790.1880.15650.21710.135-0.0834-0.07530.12530.00460.4298-0.1416-0.09580.38530.05230.4073-51.803268.0786-5.3335
51.91280.2708-0.58440.76820.03511.750.0369-0.2534-0.09020.3293-0.0484-0.1825-0.25340.425-0.03160.6232-0.1695-0.20630.46720.03710.5482-41.593269.001916.1023
64.31120.788-0.63630.6491-0.5731.27310.1497-0.3121-0.00050.4095-0.1323-0.1698-0.19330.2365-0.03550.8859-0.1276-0.220.4688-0.00670.4622-49.164356.374234.3795
73.2273-0.27920.88741.1976-0.33721.09950.2332-0.1299-0.10930.2816-0.1707-0.26530.03860.0687-0.08960.7812-0.0353-0.08820.44890.08860.3726-58.198435.381834.4325
81.0274-0.4002-0.04811.87960.87641.237-0.0257-0.05430.1217-0.04260.0227-0.0728-0.10130.05440.00680.38-0.0865-0.01590.45180.05720.2797-77.412170.6099-31.9352
91.02890.71260.21762.35160.76271.44230.02940.1342-0.04040.07230.0358-0.0214-0.01710.1341-0.09380.2615-0.01030.00610.55830.07680.3087-64.075565.3467-49.6097
101.31310.95490.22141.39750.03260.9126-0.05920.4920.0242-0.110.1421-0.0093-0.08260.2436-0.08530.33440.04810.05190.72910.03590.3273-67.853767.2277-72.8265
111.60060.735-0.04411.1848-0.45631.0399-0.03880.44280.1435-0.06760.1380.1082-0.08910.0333-0.08930.4180.08040.01250.75720.00850.3523-87.408968.2105-83.1168
121.39430.5177-0.34131.5255-0.96451.29660.00210.31190.105-0.06440.0636-0.04530.0079-0.103-0.05840.28250.0299-0.03260.6515-0.00490.3971-108.567767.6756-73.2314
131.2784-0.67070.18651.7967-0.24830.7343-0.05950.02840.12590.1554-0.0024-0.0042-0.1622-0.2080.00140.28140.0330.00750.5934-0.04240.3854-114.607173.4597-51.1607
141.4348-1.01160.49632.91180.07441.27050.0269-0.23180.06970.0902-0.02920.0509-0.0315-0.1859-0.01410.3238-0.06340.03990.48140.00340.2592-100.610669.9009-32.8398
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection details
11(chain 'A' and resid 6 through 269)
22(chain 'B' and resid 6 through 270)
33(chain 'C' and resid 6 through 270)
44(chain 'D' and resid 6 through 269)
55(chain 'E' and resid 7 through 270)
66(chain 'F' and resid 8 through 269)
77(chain 'G' and resid 6 through 269)
88(chain 'H' and resid 6 through 269)
99(chain 'I' and resid 5 through 270)
1010(chain 'J' and resid 6 through 270)
1111(chain 'K' and resid 0 through 270)
1212(chain 'L' and resid 5 through 269)
1313(chain 'M' and resid 6 through 270)
1414(chain 'N' and resid 6 through 269)

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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