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- PDB-4bjr: Crystal structure of the complex between Prokaryotic Ubiquitin-li... -

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Basic information

Entry
Database: PDB / ID: 4bjr
TitleCrystal structure of the complex between Prokaryotic Ubiquitin-like Protein Pup and its Ligase PafA
ComponentsPUP--PROTEIN LIGASE, PROKARYOTIC UBIQUITIN-LIKE PROTEIN PUP
KeywordsLIGASE / PROKARYOTIC PROTEASOME
Function / homology
Function and homology information


prokaryotic ubiquitin-like protein ligase / protein pupylation / ligase activity, forming carbon-nitrogen bonds / ubiquitin-like protein transferase activity / proteasome binding / proteasomal protein catabolic process / modification-dependent protein catabolic process / protein tag activity / magnesium ion binding / ATP binding
Similarity search - Function
Pup--protein ligase / Pup ligase/deamidase / Pup-ligase protein / Prokaryotic ubiquitin-like protein Pup / Pup-like protein
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Prokaryotic ubiquitin-like protein Pup / Pup--protein ligase
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBarandun, J. / Delley, C.L. / Ban, N. / Weber-Ban, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Crystal Structure of the Complex between Prokaryotic Ubiquitin-Like Protein Pup and its Ligase Pafa.
Authors: Barandun, J. / Delley, C.L. / Ban, N. / Weber-Ban, E.
History
DepositionApr 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Structure summary
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _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.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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUP--PROTEIN LIGASE, PROKARYOTIC UBIQUITIN-LIKE PROTEIN PUP
B: PUP--PROTEIN LIGASE, PROKARYOTIC UBIQUITIN-LIKE PROTEIN PUP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0997
Polymers115,0122
Non-polymers1,0875
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-70.1 kcal/mol
Surface area39360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.840, 84.020, 215.110
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 PUP--PROTEIN LIGASE, PROKARYOTIC UBIQUITIN-LIKE PROTEIN PUP / PROTEASOME ACCESSORY FACTOR A / PUP-CONJUGATING ENZYME / BACTERIAL UBIQUITIN-LIKE MODIFIER


Mass: 57505.828 Da / Num. of mol.: 2 / Fragment: RESIDUES PAFA 2-482, PUP 38-64 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PAFA-PUPE FUSION CONSTRUCT / Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: Q8NQE1, UniProt: Q8NQE0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.52 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 6.8
Details: 100 MM MES, PH 6.8 (RT), 150 - 200 MM SODIUM TARTRATE, 2 - 4 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→39 Å / Num. obs: 29211 / % possible obs: 99.8 % / Observed criterion σ(I): 2.44 / Redundancy: 4.9 % / Biso Wilson estimate: 50.66 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.8
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.44 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B0T

4b0t


Resolution: 2.8→39.131 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1490 5.1 %
Rwork0.2131 --
obs0.2149 29211 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→39.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7772 0 65 134 7971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127979
X-RAY DIFFRACTIONf_angle_d1.11810815
X-RAY DIFFRACTIONf_dihedral_angle_d15.4342987
X-RAY DIFFRACTIONf_chiral_restr0.0631218
X-RAY DIFFRACTIONf_plane_restr0.0061402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.89040.32921200.29012486X-RAY DIFFRACTION100
2.8904-2.99370.311320.29392486X-RAY DIFFRACTION100
2.9937-3.11350.33791360.29052482X-RAY DIFFRACTION100
3.1135-3.25510.33611390.27782467X-RAY DIFFRACTION100
3.2551-3.42660.28771230.25362494X-RAY DIFFRACTION100
3.4266-3.64120.29071430.22682501X-RAY DIFFRACTION99
3.6412-3.92210.2481220.21022519X-RAY DIFFRACTION100
3.9221-4.31630.22721510.17642490X-RAY DIFFRACTION100
4.3163-4.93980.18181340.16442550X-RAY DIFFRACTION100
4.9398-6.21970.22231400.19042562X-RAY DIFFRACTION100
6.2197-39.13480.20751500.18932684X-RAY DIFFRACTION99
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)
10.6325-0.1590.00430.78440.17790.1339-0.04340.0663-0.2341-0.19910.01840.10580.0709-0.4-0.08360.3667-0.1255-0.01080.35960.01220.344134.46310.770221.0619
20.12690.07630.17830.7953-0.06460.38110.0627-0.066-0.12550.0051-0.07110.08510.0604-0.1329-0.00780.3854-0.0516-0.06110.35380.04140.375133.32973.496125.2316
30.86280.92261.14611.82590.53741.6422-0.07650.1742-0.1286-0.56590.23-0.1920.15230.37750.04670.4555-0.04510.02280.406-0.04720.483541.0167-7.764325.1326
40.44080.27230.07360.7756-0.19980.53150.0969-0.1993-0.10710.0905-0.0710.09570.3083-0.0821-0.00050.3992-0.0782-0.00420.3720.03860.362426.6028-8.147431.9333
50.2001-0.0433-0.10820.34610.27950.2221-0.0466-0.24520.00440.28010.0631-0.0504-0.1863-0.0685-0.01170.2905-0.0845-0.01150.386-0.06950.34138.421624.513235.6464
60.7648-0.74150.19440.6688-0.44961.04170.01360.29350.5962-0.02850.0925-0.4819-0.66990.37460.05410.5443-0.07690.19930.32930.03480.520320.151640.969721.7728
71.6851-0.56270.28381.66820.87780.82870.55580.50960.243-0.3588-0.1016-0.2441-0.45130.86750.38120.0556-0.1243-0.05530.1545-0.01160.16361.761132.730327.7358
80.57780.49560.60180.38320.40151.98280.29990.005-0.03470.0930.0701-0.1140.49970.13420.27380.4196-0.04230.04080.3790.0040.2764-1.385623.20421.587
90.91570.0556-0.29180.6174-0.13780.52220.3141-0.0440.1367-0.2528-0.0936-0.169-0.0945-0.02970.31010.3222-0.00650.0750.32250.03290.30421.971234.671228.3719
103.14950.5564-0.52831.46450.83290.91730.160.25640.4311-0.5531-0.1187-0.1353-0.3337-0.4368-0.21620.51830.05050.09230.3450.00880.3709-2.062751.877225.0389
110.4535-0.0171-0.54231.11110.52910.72170.1659-0.10120.06260.0055-0.0996-0.1913-0.16820.00330.0060.2495-0.06920.03550.29520.01560.29266.173242.307137.2911
121.092-0.237-0.13880.79170.18770.59570.0237-0.2435-0.16050.0303-0.07030.2835-0.1030.072-0.42310.2658-0.0856-0.05520.20030.09070.24895.47094.471526.3735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 3 THROUGH 59 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 60 THROUGH 159 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 160 THROUGH 216 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 217 THROUGH 417 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 418 THROUGH 463 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 464 THROUGH 515 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 3 THROUGH 32 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 33 THROUGH 78 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 79 THROUGH 159 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 160 THROUGH 194 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 195 THROUGH 417 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 418 THROUGH 515 )

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