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- PDB-2cby: Crystal structure of the ATP-dependent Clp Protease proteolytic s... -

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Basic information

Entry
Database: PDB / ID: 2cby
TitleCrystal structure of the ATP-dependent Clp Protease proteolytic subunit 1 (ClpP1) from Mycobacterium tuberculosis
ComponentsATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
KeywordsHYDROLASE / SERINE PROTEASE / CLP PROTEASE / PROTEOLYTIC SUBUNIT / ENDOPEPTIDASE / MYCOBACTERIUM TUBERCULOSIS / ATP-DEPENDENT PROTEASE
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit 1 / ATP-dependent Clp protease proteolytic subunit 1
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMate, M.J. / Portnoi, D. / Alzari, P.M. / Ortiz-Lombardia, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Insights Into the Inter-Ring Plasticity of Caseinolytic Proteases from the X-Ray Structure of Mycobacterium Tuberculosis Clpp1.
Authors: Ingvarsson, H. / Mate, M.J. / Hogbom, M. / Portnoi, D. / Benaroudj, N. / Alzari, P.M. / Ortiz-Lombardia, M. / Unge, T.
History
DepositionJan 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
B: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
C: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
D: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
E: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
F: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
G: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1


Theoretical massNumber of molelcules
Total (without water)159,5927
Polymers159,5927
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)178.255, 178.255, 264.914
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsCLPP ENDOPEPTIDASES ARE KNOWN TO BE TETRADECAMERICAND THIS IS THE MULTIMERIC STATE FOUND IN THISSTRUCTURE.HOWEVER, IN THIS PROTEIN, GEL FILTRATION AND INTER-COMPLEX REGIONS BETWEEN THE TWO HEPTAMERIC RINGS WOULDINDICATE THAT THE OLIGOMER IS LIKELY TO BE HEPTAMERICIN SOLUTION.IN ORDER TO GENERATE THE 14-MER, THE FOLLOWINGTRANSFORMATION NEEDS TO BE APPLIED TO ALL THE SEVENCHAINS IN THIS FILE.BIOMT1 2 0.500000 -0.866025 0. 000000 89.12738BIOMT2 2 -0.866025 -0. 500000 0.000000 154.37311BIOMT3 2 0. 000000 0.000000 -1.000000 220.76231

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Components

#1: Protein
ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1 / ENDOPEPTIDASE CLPP 1


Mass: 22798.818 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: INSTITUT PASTEUR COLLECTION / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A526, UniProt: P9WPC5*PLUS, endopeptidase Clp
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCLEAVES PEPTIDES IN VARIOUS PROTEINS IN A PROCESS THAT REQUIRES ATP HYDROLYSIS. HAS A CHYMOTRYPSIN- ...CLEAVES PEPTIDES IN VARIOUS PROTEINS IN A PROCESS THAT REQUIRES ATP HYDROLYSIS. HAS A CHYMOTRYPSIN-LIKE ACTIVITY. PLAYS A MAJOR ROLE IN THE DEGRADATION OF MISFOLDED PROTEINS.

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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: 3.83 Å3/Da / Density % sol: 67.91 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: THE PROTEIN WAS CRYSTALLISED BY THE VAPOUR DIFFUSION METHOD IN HANGING DROPS CONTAINING A 1:1 MIXTURE OF 3 MG/ML PROTEIN SOLUTION (IN 50 MM TRIS-HCL PH 8) AND RESERVOIR SOLUTION INCLUDING 1 ...Details: THE PROTEIN WAS CRYSTALLISED BY THE VAPOUR DIFFUSION METHOD IN HANGING DROPS CONTAINING A 1:1 MIXTURE OF 3 MG/ML PROTEIN SOLUTION (IN 50 MM TRIS-HCL PH 8) AND RESERVOIR SOLUTION INCLUDING 1 M AMMONIUM SULPHATE IN 0.1 M HEPES PH 8.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93366
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93366 Å / Relative weight: 1
ReflectionResolution: 2.6→76.7 Å / Num. obs: 76728 / % possible obs: 100 % / Redundancy: 22.2 % / Biso Wilson estimate: 40.12 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 24.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 6.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TYF

1tyf


Resolution: 2.6→154.3 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 12.914 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL REGION OF EACH MONOMER, UP TO RESIDUE LEU14 IS NOT VISIBLE IN THE ELECTRON DENSITY MAP AND HAS NOT BEEN MODELLED. THE REGION ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL REGION OF EACH MONOMER, UP TO RESIDUE LEU14 IS NOT VISIBLE IN THE ELECTRON DENSITY MAP AND HAS NOT BEEN MODELLED. THE REGION COMPRISING RESIDUES LEU126 TO D135 OF EACH MONOMER IS NOT VISIBLE IN THE ELECTRON DENSITY MAP AND HAS NOT BEEN MODELLED. THE 13-17 C-TERMINAL RESIDUES OF THE MONOMER ARE NOT VISIBLE IN THE ELECTRON DENSITY AND HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3895 5.12 %RANDOM
Rwork0.192 ---
obs0.194 76647 100 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 19.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.872 Å20.436 Å20 Å2
2--0.872 Å20 Å2
3----1.307 Å2
Refinement stepCycle: LAST / Resolution: 2.6→154.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9149 0 0 301 9450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.481.96512557
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2151171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91223.735415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.468151604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2331569
X-RAY DIFFRACTIONr_chiral_restr0.1020.21431
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026958
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.24081
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.26414
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2398
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8051.56054
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33329363
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.31833658
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7984.53194
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 11.6→154.3 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.464 47
Rwork0.399 973
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)
12.2703-0.7011-0.06051.01740.09812.2256-0.01510.0645-0.00440.01230.0002-0.02310.19320.2260.015-0.00110.0226-0.0133-0.07640.0445-0.035935.6324117.811188.0467
21.3906-0.1736-0.22880.5879-0.21942.5063-0.0682-0.1597-0.10450.0439-0.01930.02840.23930.05720.08750.02-0.001-0.0126-0.12540.0397-0.045313.552123.0841104.7082
32.2509-0.02430.46791.0942-0.92821.9450.00710.1547-0.0469-0.1247-0.0083-0.01250.08280.07080.0012-0.0410.03790.0107-0.1189-0.0248-0.08798.7022114.6512131.2186
42.2775-0.6444-0.32051.2038-0.42981.18690.02210.1287-0.0852-0.091-0.0563-0.130.13580.09520.0342-0.07420.03840.0054-0.1037-0.0278-0.090124.735898.5619147.597
51.692-0.4368-0.70731.3806-0.49481.8130.0160.06560.02690.04880.09310.0796-0.0474-0.0801-0.1092-0.11690.0707-0.028-0.0192-0.0114-0.052349.378586.1273141.247
61.0966-0.3231-0.2591.4281-0.54532.48710.01860.17950.0197-0.16780.07790.0603-0.1054-0.1453-0.0965-0.07780.0576-0.03220.0102-0.0071-0.012664.486288.1153117.5019
71.405-1.12890.15321.84370.10323.0409-0.07550.07230.0747-0.02780.02210.0673-0.07820.02410.0534-0.04470.01490.00530.04120.03710.015858.3852102.496993.4712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 193
2X-RAY DIFFRACTION2B15 - 194
3X-RAY DIFFRACTION3C15 - 193
4X-RAY DIFFRACTION4D15 - 195
5X-RAY DIFFRACTION5E15 - 193
6X-RAY DIFFRACTION6F15 - 194
7X-RAY DIFFRACTION7G15 - 191

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