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Basic information

Entry
Database: PDB / ID: 2wfw
TitleStructure and activity of the N-terminal substrate recognition domains in proteasomal ATPases - The Arc domain structure
ComponentsARC
KeywordsATP-BINDING PROTEIN / PROTEASOMAL ATPASES / PAN / ARC / AAA / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / CTPase activity / proteasome complex / proteasomal protein catabolic process / modification-dependent protein catabolic process / ATP hydrolysis activity / ATP binding
Similarity search - Function
Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleic acid-binding proteins / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleic acid-binding proteins / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Proteasome-associated ATPase
Similarity search - Component
Biological speciesRHODOCOCCUS ERYTHROPOLIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsDjuranovic, S. / Hartmann, M.D. / Habeck, M. / Ursinus, A. / Zwickl, P. / Martin, J. / Lupas, A.N. / Zeth, K.
CitationJournal: Mol.Cell / Year: 2009
Title: Structure and Activity of the N-Terminal Substrate Recognition Domains in Proteasomal Atpases.
Authors: Djuranovic, S. / Hartmann, M.D. / Habeck, M. / Ursinus, A. / Zwickl, P. / Martin, J. / Lupas, A.N. / Zeth, K.
History
DepositionApr 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 15-STRANDED BARREL THIS IS REPRESENTED BY A 16-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARC
B: ARC
C: ARC


Theoretical massNumber of molelcules
Total (without water)49,8233
Polymers49,8233
Non-polymers00
Water8,305461
1
A: ARC
B: ARC
C: ARC

A: ARC
B: ARC
C: ARC


Theoretical massNumber of molelcules
Total (without water)99,6466
Polymers99,6466
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area10210 Å2
ΔGint-28.18 kcal/mol
Surface area34740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.330, 100.330, 88.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 81 - 160 / Label seq-ID: 8 - 87

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein ARC


Mass: 16607.674 Da / Num. of mol.: 3 / Fragment: RESIDUES 73-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS ERYTHROPOLIS (bacteria) / Plasmid: PET30B (NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O50202
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.05 MM CACL2, 0.1 M BIS-TRIS PH 6.5, 30% PEG550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 64443 / % possible obs: 95.2 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.7
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.2 / % possible all: 78.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.843 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24641 3222 5 %RANDOM
Rwork0.20825 ---
obs0.21011 61206 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.377 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 0 461 3268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222881
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.983926
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.415381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.26723.898118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2615477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3611523
X-RAY DIFFRACTIONr_chiral_restr0.1370.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022129
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.21361
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22000
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2329
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0731.51915
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71522998
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.44231075
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7464.5921
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 585 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.45
2Bloose positional0.365
3Cloose positional0.545
1Aloose thermal1.5310
2Bloose thermal1.3110
3Cloose thermal1.2810
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 132 -
Rwork0.287 2491 -
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)
11.5791-0.1116-0.2661.5829-0.39811.3246-0.02040.00070.00290.0590.06620.0533-0.11440.0037-0.04590.0079-0.00230.018-0.02740.0176-0.071852.77522.63116.578
22.9773-0.573-0.41662.7898-2.14552.2939-0.1883-0.0728-0.13410.3179-0.0681-0.1207-0.15210.23390.2564-0.0014-0.0711-0.08090.02670.0249-0.074272.49319.31620.667
31.35270.1609-0.81922.64190.8662.9217-0.0448-0.1588-0.16110.1892-0.0719-0.29430.01730.33050.1166-0.0683-0.055-0.0444-0.00420.0489-0.041874.76622.03711.502
44.1721.16851.02383.1407-0.63234.19550.0457-0.0687-0.09330.3923-0.225-0.3097-0.30090.44510.17930.0187-0.0964-0.07760.04840.0633-0.039774.20920.43220.548
51.19680.17310.51761.8866-0.08081.1171-0.01520.02660.0152-0.19660.04050.09070.0702-0.0365-0.02530.0147-0.0497-0.0056-0.01960.006-0.071755.85913.393-3.458
63.9321-0.2767-0.15247.43651.40642.00820.08510.02030.0974-0.44310.117-0.7608-0.04030.2568-0.2022-0.0705-0.02670.0985-0.0014-0.0018-0.015575.258.083-5.69
73.38230.60480.14085.49661.21732.17880.0278-0.10580.0369-0.13750.0152-0.1784-0.04960.0733-0.043-0.0516-0.04310.04360.00240.0019-0.034871.37113.253-0.578
81.7259-0.8041-0.3710.8832-0.36550.6495-0.0216-0.0885-0.04260.20980.0467-0.0137-0.12990.0316-0.02510.07450.0452-0.007-0.0153-0.0022-0.077656.468.8535.735
93.42840.9258-2.26322.1913-3.04736.6671-0.0188-0.01420.10730.2833-0.2724-0.4274-0.64670.57760.2912-0.0035-0.0821-0.10230.02320.0444-0.048275.1213.20531.297
104.5939-0.83530.72753.7645-1.51523.48160.07310.0778-0.01060.3058-0.1832-0.2325-0.23320.18010.1102-0.0038-0.0063-0.0678-0.00520.0319-0.05771.4646.32833.204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 135
2X-RAY DIFFRACTION2A136 - 147
3X-RAY DIFFRACTION3A148 - 176
4X-RAY DIFFRACTION4A200 - 220
5X-RAY DIFFRACTION5B80 - 146
6X-RAY DIFFRACTION6B147 - 174
7X-RAY DIFFRACTION7B200 - 214
8X-RAY DIFFRACTION8C80 - 146
9X-RAY DIFFRACTION9C147 - 175
10X-RAY DIFFRACTION10C200 - 214

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