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- PDB-4b0s: Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiq... -

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Basic information

Entry
Database: PDB / ID: 4b0s
TitleStructure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ATP
ComponentsDEAMIDASE-DEPUPYLASE DOP
KeywordsHYDROLASE / PUPYLATION / PROKARYOTIC UBIQUITIN-LIKE PROTEIN / PROTEASOME
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on peptide bonds (peptidases) / proteasomal protein catabolic process / modification-dependent protein catabolic process / peptidase activity / ATP binding / metal ion binding
Similarity search - Function
Pup deamidase / Pup ligase/deamidase / Pup-ligase protein
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Depupylase
Similarity search - Component
Biological speciesACIDOTHERMUS CELLULOLYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsOzcelik, D. / Barandun, J. / Schmitz, N. / Sutter, M. / Guth, E. / Damberger, F.F. / Allain, F.H.-T. / Ban, N. / Weber-Ban, E.
CitationJournal: Nat.Commun. / Year: 2012
Title: Structures of Pup Ligase Pafa and Depupylase Dop from the Prokaryotic Ubiquitin-Like Modification Pathway.
Authors: Ozcelik, D. / Barandun, J. / Schmitz, N. / Sutter, M. / Guth, E. / Damberger, F.F. / Allain, F.H.-T. / Ban, N. / Weber-Ban, E.
History
DepositionJul 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Atomic model
Revision 1.2Feb 27, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Apr 1, 2020Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_conf / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_sheet_hbond.range_1_auth_atom_id ..._pdbx_database_status.status_code_sf / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEAMIDASE-DEPUPYLASE DOP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6834
Polymers57,1271
Non-polymers5563
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.360, 70.410, 93.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DEAMIDASE-DEPUPYLASE DOP


Mass: 57127.176 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-501
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDOTHERMUS CELLULOLYTICUS (bacteria) / Strain: 11B / Plasmid: PET EXPRESSION SYSTEM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: A0LU48, Hydrolases; Acting on peptide bonds (peptidases), Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.86 Å3/Da / Density % sol: 33.74 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 100 MM HEPES-HCL PH 7.2 (298 K), 14 % (V/V) PEG-3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→47 Å / Num. obs: 10376 / % possible obs: 98.4 % / Observed criterion σ(I): 2.89 / Redundancy: 3.4 % / Biso Wilson estimate: 56.26 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.69
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.89 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→47.902 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 26.29 / Stereochemistry target values: ML / Details: RESIDUES 37-80 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2461 495 4.8 %
Rwork0.1894 --
obs0.1921 10375 98.4 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.22 Å2 / ksol: 0.348 e/Å3
Refinement stepCycle: LAST / Resolution: 2.85→47.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 33 5 3653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033732
X-RAY DIFFRACTIONf_angle_d0.7895062
X-RAY DIFFRACTIONf_dihedral_angle_d12.3691390
X-RAY DIFFRACTIONf_chiral_restr0.047555
X-RAY DIFFRACTIONf_plane_restr0.003665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.13680.30341310.24572395X-RAY DIFFRACTION98
3.1368-3.59050.30511130.21052438X-RAY DIFFRACTION98
3.5905-4.52310.23741340.17192452X-RAY DIFFRACTION98
4.5231-47.90920.20821170.17682595X-RAY DIFFRACTION98
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)
10.1241-0.05320.03750.08030.0730.059-0.23490.02810.26850.01140.0221-0.1152-0.1456-0.1689-0.0060.2503-0.0324-0.07960.24540.01060.332-6.036915.7739-19.139
20.20020.1095-0.15820.3537-0.09260.472-0.1750.06470.02140.30420.04920.17370.0245-0.0299-0.06090.18830.01870.05150.1819-0.01830.1807-24.64575.0911-14.1653
30.16070.1619-0.1190.122-0.18020.0809-0.14950.1467-0.0262-0.04910.1016-0.231-0.06120.1043-00.2734-0.0325-0.03260.2404-0.00560.2007-8.622716.5674-34.9104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 153)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 154 THROUGH 394)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 395 THROUGH 500)

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