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- PDB-6dfk: Crystal structure of the 11S subunit of the Plasmodium falciparum... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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Processing

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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)

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