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- PDB-4b0r: Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiq... -

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Basic information

Entry
Database: PDB / ID: 4b0r
TitleStructure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway
ComponentsDEAMIDASE-DEPUPYLASE DOP
KeywordsHYDROLASE / PUPYLATION / DEPUPYLATION / PROTEASOME
Function / homology
Function and homology information


protein pupylation / 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
Biological speciesACIDOTHERMUS CELLULOLYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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. / 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 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DEAMIDASE-DEPUPYLASE DOP


Theoretical massNumber of molelcules
Total (without water)57,1271
Polymers57,1271
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.550, 71.470, 96.120
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACIDOTHERMUS CELLULOLYTICUS (bacteria) / Strain: 11B / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1.97 Å3/Da / Density % sol: 37.6 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 100 MM HEPES-HCL PH 7.2, 14 % (V/V) PEG-3350, 298 K

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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: 2.6→59 Å / Num. obs: 14518 / % possible obs: 99.2 % / Observed criterion σ(I): 2.01 / Redundancy: 3.6 % / Biso Wilson estimate: 53.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.59
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.01 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→57.353 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 730 5 %
Rwork0.194 --
obs0.1962 14513 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.174 Å2 / ksol: 0.249 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→57.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 0 29 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033690
X-RAY DIFFRACTIONf_angle_d0.8085008
X-RAY DIFFRACTIONf_dihedral_angle_d11.9481377
X-RAY DIFFRACTIONf_chiral_restr0.062551
X-RAY DIFFRACTIONf_plane_restr0.003664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80070.35321550.26852695X-RAY DIFFRACTION100
2.8007-3.08260.28261500.24562720X-RAY DIFFRACTION100
3.0826-3.52860.28911490.22272723X-RAY DIFFRACTION99
3.5286-4.44540.21781300.17242779X-RAY DIFFRACTION99
4.4454-57.3670.1941460.17012866X-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)
10.37710.3284-0.07680.5284-0.17170.339-0.0725-0.07350.0972-0.00860.12510.1378-0.1171-0.196900.33290.0245-0.03290.46530.02860.41246.350716.553619.4197
20.737-0.13590.32270.8-0.62880.7072-0.05670.03570.0928-0.2656-0.0047-0.168-0.03690.1397-00.39450.0050.03480.37080.01330.363727.314610.511814.3967
30.6097-0.2760.40251.1367-0.33591.025-0.0428-0.1569-0.04170.02330.0486-0.02450.1943-0.14100.2886-0.007-0.00090.32920.02620.339214.62877.424925.6894
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 305 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 306 THROUGH 500 )

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