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- PDB-5lrt: Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiq... -

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Basic information

Entry
Database: PDB / ID: 5lrt
TitleStructure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ADP and Phosphate
ComponentsDepupylase
KeywordsHYDROLASE / Complex
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
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Depupylase
Similarity search - Component
Biological speciesAcidothermus cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBolten, M. / Vahlensieck, C. / Lipp, C. / Leibundgut, M. / Ban, N. / Weber-Ban, E.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Depupylase Dop Requires Inorganic Phosphate in the Active Site for Catalysis.
Authors: Bolten, M. / Vahlensieck, C. / Lipp, C. / Leibundgut, M. / Ban, N. / Weber-Ban, E.
History
DepositionAug 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Depupylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,62012
Polymers57,2881
Non-polymers1,33111
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-54 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.398, 72.398, 215.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Depupylase


Mass: 57288.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidothermus cellulolyticus (strain ATCC 43068 / 11B) (bacteria)
Gene: dop, Acel_1186 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0LU48, Hydrolases; Acting on peptide bonds (peptidases)

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Non-polymers , 8 types, 235 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18-23% (w/v) PEG 3350, 100mM bis-tris propane pH 8.25-9.0 at 20 degC, 200mM KSCN, 20mM MgCl2 and 5mM ATP
PH range: 8.25 - 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.85→36.2 Å / Num. obs: 56972 / % possible obs: 100 % / Redundancy: 8.9 % / Biso Wilson estimate: 39.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.016 / Rrim(I) all: 0.047 / Net I/σ(I): 24.3 / Num. measured all: 506782
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.85-1.8991.4980.6151100
9.06-36.28.40.0221198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.27 Å36.2 Å
Translation7.27 Å36.2 Å

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHASER2.6.0phasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSVERSION March 30, 2013data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4b0r

4b0r


Resolution: 1.85→36.199 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.34
RfactorNum. reflection% reflection
Rfree0.1977 2880 5.06 %
Rwork0.1665 --
obs0.168 56895 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.57 Å2 / Biso mean: 49.5952 Å2 / Biso min: 25.1 Å2
Refinement stepCycle: final / Resolution: 1.85→36.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 83 224 3943
Biso mean--52.69 53.07 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113849
X-RAY DIFFRACTIONf_angle_d1.1275229
X-RAY DIFFRACTIONf_chiral_restr0.066574
X-RAY DIFFRACTIONf_plane_restr0.008684
X-RAY DIFFRACTIONf_dihedral_angle_d14.9722336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8501-1.88040.36941250.318524972622
1.8804-1.91280.31441500.303625522702
1.9128-1.94760.26791270.250325332660
1.9476-1.98510.24311610.229524942655
1.9851-2.02560.26931290.202225742703
2.0256-2.06960.19681390.194225052644
2.0696-2.11780.21411370.190425322669
2.1178-2.17070.18681300.176125402670
2.1707-2.22940.20741400.17225502690
2.2294-2.2950.20711360.165425442680
2.295-2.36910.22451270.166425692696
2.3691-2.45370.19391220.161425582680
2.4537-2.55190.16031440.159525652709
2.5519-2.6680.21381320.157525852717
2.668-2.80870.22331610.167625342695
2.8087-2.98450.21961400.169725792719
2.9845-3.21490.21221370.175225902727
3.2149-3.53810.20511300.167626012731
3.5381-4.04950.17641540.156126212775
4.0495-5.09970.17341250.135426722797
5.0997-36.20590.1791340.169728202954
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)
11.9119-0.28411.76653.19570.54861.9218-0.19250.1851-0.02660.17430.3620.12750.0562-0.29130.02470.28790.01410.0630.3272-0.05260.3567-9.503466.652825.1164
20.2921-0.40340.00530.60950.17930.604-0.13750.11530.50370.62760.18630.3176-0.4088-0.23420.00020.56580.10140.07020.5179-0.06940.4871-12.007176.529733.7519
31.43190.91370.90823.06880.28621.89220.0130.04520.05620.31580.0786-0.017-0.22870.0668-0.00020.2873-0.01190.02310.3194-0.03140.3055-3.763171.123827.7499
40.2502-0.0337-0.00490.104-0.10320.11560.0636-0.82390.30010.8767-0.01520.0168-0.2707-0.35980.00050.68690.02410.11920.6638-0.10220.469-14.708766.79640.0921
51.19720.27091.0262.25890.99681.6513-0.0920.5741-0.1826-0.26740.13290.1976-0.1492-0.13330.00750.31-0.02730.02230.5143-0.09120.3221-11.865861.084511.6646
60.0156-0.0199-0.00390.02630.00940.0194-0.04680.16360.1036-0.11820.15110.4856-0.1012-0.0552-0.00130.7211-0.02460.03670.7214-0.07961.0215-21.217469.497812.2116
71.26380.08290.51021.42020.55761.3894-0.18810.69270.0205-0.44210.2824-0.2469-0.41610.33570.01280.4222-0.09590.06340.586-0.04590.3398-3.168268.61199.371
80.3144-0.06710.11570.4362-0.04050.2712-0.04760.8919-0.5384-0.3130.1522-0.11090.2240.26450.03750.4449-0.05810.02170.7694-0.28820.5026-12.363151.61923.0114
90.7091-0.27870.67861.020.37941.13080.01450.8143-0.2767-0.60960.1126-0.35090.01430.6396-0.14920.43440.04230.22450.9348-0.57940.60944.979254.32253.7142
100.93070.4901-0.60441.5091-0.38091.93270.07280.0148-0.45610.3403-0.008-0.21810.3750.0376-0.00020.33390.0364-0.05120.3326-0.05330.5201-5.781250.006428.109
112.01340.83570.63020.85131.00211.4909-0.32010.27510.708-0.16510.2673-0.2519-0.47760.3667-0.00040.4572-0.1381-0.00460.44020.00320.51046.407787.921325.2276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:20)A1 - 20
2X-RAY DIFFRACTION2(chain A and resid 21:42)A21 - 43
3X-RAY DIFFRACTION3(chain A and resid 79:130)A79 - 130
4X-RAY DIFFRACTION4(chain A and resid 131:141)A131 - 141
5X-RAY DIFFRACTION5(chain A and resid 142:215)A142 - 215
6X-RAY DIFFRACTION6(chain A and resid 216:220)A216 - 220
7X-RAY DIFFRACTION7(chain A and resid 221:273)A221 - 273
8X-RAY DIFFRACTION8(chain A and resid 274:299)A274 - 299
9X-RAY DIFFRACTION9(chain A and resid 300:353)A300 - 353
10X-RAY DIFFRACTION10(chain A and resid 354:425)A354 - 425
11X-RAY DIFFRACTION11(chain A and resid 426:500)A426 - 500

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