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- PDB-5hbn: ClpC N-terminal domain with bound phospho-arginine -

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Basic information

Entry
Database: PDB / ID: 5hbn
TitleClpC N-terminal domain with bound phospho-arginine
ComponentsNegative regulator of genetic competence ClpC/MecB
KeywordsHYDROLASE / Clp protease / degradation tag / protein phosphorylation / phospho-residue binding site
Function / homology
Function and homology information


establishment of competence for transformation / ATP hydrolysis activity / ATP binding
Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain ...Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / phospho-arginine / Negative regulator of genetic competence ClpC/MecB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å
AuthorsSuskiewicz, M.J. / Clausen, T.
CitationJournal: Nature / Year: 2016
Title: Arginine phosphorylation marks proteins for degradation by a Clp protease.
Authors: Trentini, D.B. / Suskiewicz, M.J. / Heuck, A. / Kurzbauer, R. / Deszcz, L. / Mechtler, K. / Clausen, T.
History
DepositionJan 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_1
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Negative regulator of genetic competence ClpC/MecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1939
Polymers17,1461
Non-polymers1,0488
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-40 kcal/mol
Surface area7520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.600, 84.600, 29.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Negative regulator of genetic competence ClpC/MecB


Mass: 17145.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: clpC, mecB, BSU00860 / Production host: Escherichia coli (E. coli) / References: UniProt: P37571
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RPI / phospho-arginine


Type: L-peptide linking / Mass: 254.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O5P
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.8 Å3/Da / Density % sol: 31.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: The optimized crystallization solution contained 13.5% w/w polyethylene glycol 4000, 500 mM ammonium sulphate, and 100 mM sodium acetate at pH 5. Hexagonal crystals of space group P 6(5) ...Details: The optimized crystallization solution contained 13.5% w/w polyethylene glycol 4000, 500 mM ammonium sulphate, and 100 mM sodium acetate at pH 5. Hexagonal crystals of space group P 6(5) formed overnight at 19C and were cryo-protected in 40% polyethylene glycol 400, 20 mM Tris pH 8, and 6 mM pArgAA prior to being flash-frozen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.602→42.3 Å / Num. obs: 16041 / % possible obs: 98.19 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.06169 / Rrim(I) all: 0.06347 / Net I/σ(I): 29.81

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Processing

Software
NameVersionClassification
PHENIX(dev_2356: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERPhaser-2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y1Q

2y1q


Resolution: 1.602→42.3 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 17.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.166 1585 9.88 %
Rwork0.1447 --
obs0.1469 16041 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.602→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 61 40 1206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091228
X-RAY DIFFRACTIONf_angle_d1.081655
X-RAY DIFFRACTIONf_dihedral_angle_d21.287737
X-RAY DIFFRACTIONf_chiral_restr0.053183
X-RAY DIFFRACTIONf_plane_restr0.006214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6021-1.65390.2591170.19641088X-RAY DIFFRACTION82
1.6539-1.7130.24471410.1751298X-RAY DIFFRACTION99
1.713-1.78160.21841480.17011331X-RAY DIFFRACTION100
1.7816-1.86260.16671420.14381329X-RAY DIFFRACTION100
1.8626-1.96080.18691440.12711320X-RAY DIFFRACTION100
1.9608-2.08370.17141520.12011328X-RAY DIFFRACTION100
2.0837-2.24460.15551450.11391325X-RAY DIFFRACTION100
2.2446-2.47040.14761470.11691341X-RAY DIFFRACTION100
2.4704-2.82780.15651470.12491343X-RAY DIFFRACTION100
2.8278-3.56250.14661500.14661357X-RAY DIFFRACTION100
3.5625-42.31470.16781520.1661396X-RAY DIFFRACTION100

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