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- PDB-5eqt: crystal structure of the ATPase domain of PAN from Pyrococcus hor... -

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Basic information

Entry
Database: PDB / ID: 5eqt
Titlecrystal structure of the ATPase domain of PAN from Pyrococcus horikoshii
ComponentsProteasome-activating nucleotidase
KeywordsHYDROLASE / AAA+ATPase / UNFOLDASE / COMPLEX
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / proteasome-activating activity / protein unfolding / proteasomal protein catabolic process / ATP binding / cytoplasm
Similarity search - Function
26S proteasome regulatory subunit P45-like / Proteasome-activating nucleotidase PAN / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 ...26S proteasome regulatory subunit P45-like / Proteasome-activating nucleotidase PAN / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Proteasome-activating nucleotidase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.943 Å
AuthorsColombo, M.
Funding support France, 1items
OrganizationGrant numberCountry
Centre Nationale de la Recherche ScientifiqueANR-12-BSV8-0019-0 France
CitationJournal: To Be Published
Title: crystal structure of the ATPase domain of PAN from Pyrococcus horikoshii
Authors: Colombo, M. / Ibrahim, Z. / Flament, D. / Hartlein, M. / Teixeira, S. / Girard, E. / Gabel, F. / Franzetti, B.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_remark / pdbx_data_processing_status ...database_PDB_remark / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
Item: _database_PDB_remark.text
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasome-activating nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2444
Polymers28,6611
Non-polymers5823
Water32418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-17 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.344, 46.488, 56.428
Angle α, β, γ (deg.)90.000, 115.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Proteasome-activating nucleotidase / PAN / Proteasomal ATPase / Proteasome regulatory ATPase / Proteasome regulatory particle


Mass: 28661.281 Da / Num. of mol.: 1 / Fragment: UNP residues 136-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: pan, PH0201 / Production host: Escherichia coli (E. coli) / References: UniProt: O57940
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: NaCH3COO 0.1 M pH 5.5, NH4PO4 0.6 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.943→47.946 Å / Num. all: 19463 / Num. obs: 19463 / % possible obs: 97.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 44.06 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Rsym value: 0.072 / Net I/av σ(I): 5.533 / Net I/σ(I): 9.7 / Num. measured all: 132669
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
1.94-2.056.41.2480.61709026870.5761.2481.193.1
2.05-2.177.10.6771.11887126580.2910.6772.397.5
2.17-2.326.90.4081.81736325120.1790.4083.397.8
2.32-2.516.70.2373.11555023350.1060.237597.7
2.51-2.757.10.1444.81554821760.0610.1447.898.6
2.75-3.076.80.0986.71361619950.0420.09811.499.1
3.07-3.556.90.0728.81207417570.030.07218.199.4
3.55-4.356.90.05710.81042815060.0240.05724.699.5
4.35-6.156.70.0512.6781411670.0210.0526.699.4
6.15-47.9466.40.04611.943156700.020.04628.999.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H4M, chain A

3h4m


Resolution: 1.943→47.948 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 918 4.72 %
Rwork0.223 18529 -
obs0.2237 19447 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.64 Å2 / Biso mean: 68.8708 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.943→47.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 39 18 2009
Biso mean--69.18 61.67 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172017
X-RAY DIFFRACTIONf_angle_d1.6212722
X-RAY DIFFRACTIONf_chiral_restr0.093311
X-RAY DIFFRACTIONf_plane_restr0.009350
X-RAY DIFFRACTIONf_dihedral_angle_d20.512786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9434-2.04590.44031200.39932501262193
2.0459-2.17410.32511600.31652584274497
2.1741-2.34190.34591420.27312617275997
2.3419-2.57760.27971160.26842660277698
2.5776-2.95050.31331160.26362686280298
2.9505-3.71720.2531230.23032694281799
3.7172-47.96250.17821410.17782787292899
Refinement TLS params.Method: refined / Origin x: -27.8078 Å / Origin y: -6.7317 Å / Origin z: 21.9875 Å
111213212223313233
T0.3013 Å2-0.0771 Å20.0066 Å2-0.3527 Å20.0123 Å2--0.3822 Å2
L1.8302 °20.1424 °2-0.6829 °2-1.7045 °2-0.6177 °2--5.7689 °2
S0.1154 Å °-0.0821 Å °0.0296 Å °0.0277 Å °0.0238 Å °0.0789 Å °0.061 Å °-0.4277 Å °-0.1264 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA102 - 358
2X-RAY DIFFRACTION1allB439
3X-RAY DIFFRACTION1allC1 - 20
4X-RAY DIFFRACTION1allE1
5X-RAY DIFFRACTION1allF1

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