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- PDB-2ce3: CRYSTAL STRUCTURE OF THE ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC S... -

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Basic information

Entry
Database: PDB / ID: 2ce3
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 complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / plasma membrane / cytosol / cytoplasm
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
AuthorsSegelke, B. / Kim, C.Y. / Ortiz-Lombardia, M. / Alzari, P.M. / Lekin, T.
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
DepositionFeb 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 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: 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
H: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
I: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
J: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
K: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
L: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
M: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
N: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1


Theoretical massNumber of molelcules
Total (without water)304,18714
Polymers304,18714
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.719, 168.948, 104.364
Angle α, β, γ (deg.)90.00, 114.83, 90.00
Int Tables number4
Space group name H-MP1211
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.

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Components

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


Mass: 21727.664 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: INSTITUT PASTEUR COLLECTION / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P0A526, UniProt: P9WPC5*PLUS, endopeptidase Clp
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.32 Å3/Da / Density % sol: 47 %
Description: STRUCTURE DETERMINED FROM COORDINATES OF SAME PROTEIN IN A DIFFERENT SPACE GROUP AT LOWER RESOLUTION
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: THE PROTEIN WAS CRYSTALLIZED BY THE SITTING DROP METHOD WITH 400NL PROTEIN PLUS 400NL MOTHERLIQUOR AND 100UL RESERVOIR. CONDITION WAS IDENTIFIED USING A SET OF RANDOM CONDITIONS GENERATED ...Details: THE PROTEIN WAS CRYSTALLIZED BY THE SITTING DROP METHOD WITH 400NL PROTEIN PLUS 400NL MOTHERLIQUOR AND 100UL RESERVOIR. CONDITION WAS IDENTIFIED USING A SET OF RANDOM CONDITIONS GENERATED WITH CRYSTOOL SOFTWARE AND OPTIMIZED TO 9.576% (W/V) PEG 2000 0.2M LITHIUM SULFATE 0.1M MOPS (4-MORPHOLINEPROPANESULFONIC ACID) PH 6.5 WITH CRYSTOOL BY REDUCING THE PARAMETER SPACE TO THE REAGENTS UTILIZED. CRYSTALS SHOWED AFTER 2 DAYS

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→49.5 Å / Num. obs: 90593 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CBY

2cby


Resolution: 2.6→169.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 26.043 / SU ML: 0.255 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.637 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 4542 5.04 %RANDOM
Rwork0.202 ---
obs0.205 90592 95.7 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.23 Å2
Baniso -1Baniso -2Baniso -3
1-6.669 Å20 Å2-0.409 Å2
2---5.613 Å20 Å2
3----1.399 Å2
Refinement stepCycle: LAST / Resolution: 2.6→169.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18064 0 0 117 18181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02218421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.96524891
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32452328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11223.886821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.183153179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.12615129
X-RAY DIFFRACTIONr_chiral_restr0.0910.22839
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213787
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.28726
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.212810
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2640
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.214
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5521.511966
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95218552
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.49437255
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4054.56332
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: 11.59→169.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.406 60
Rwork0.339 1035
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)
12.6718-2.69081.13076.24420.01313.83240.34590.14260.0698-0.904-0.2831-0.10290.4281-0.0407-0.0628-0.09210.03680.2013-0.12710.0201-0.10530.902811.9229-6.0201
21.7734-2.01990.58474.5553-0.25973.9599-0.0075-0.1606-0.0111-0.1220.1076-0.06080.364-0.1767-0.1-0.4333-0.04920.0798-0.17360.0115-0.0672-5.38730.69214.0228
33.5394-3.3595-1.18526.20490.44142.9661-0.0668-0.0328-0.33980.41180.00360.26590.4002-0.11890.0632-0.0925-0.0303-0.0087-0.1315-0.0766-0.143-9.638226.629741.5687
43.22060.8473-2.35376.1246-0.7244.28140.2117-0.00550.07740.6686-0.04890.2463-0.3892-0.234-0.16280.1965-0.0062-0.101-0.0719-0.0256-0.1875-9.51382.235755.7597
52.67192.1569-0.71875.03771.19772.74330.02760.08890.00920.52950.0525-0.0297-0.17-0.0939-0.0801-0.08770.0645-0.1648-0.05750.0684-0.1603-5.2366-23.70945.9247
61.99831.61260.00654.2840.13715.3083-0.08740.0171-0.08230.33870.0223-0.0241-0.0693-0.15180.0651-0.39960.0746-0.001-0.1233-0.0241-0.07710.3776-31.955619.3774
71.00050.58061.06586.320.98474.7701-0.0194-0.08670.1441-0.3905-0.07820.0894-0.5844-0.3910.0976-0.39660.10380.0649-0.1006-0.0478-0.09873.3009-16.0275-3.7461
82.36841.8002-0.36276.548-0.76013.83450.2267-0.07810.21691.1168-0.1690.426-0.02760.1926-0.0577-0.0960.07240.1132-0.02860.0265-0.0386-50.759523.309131.7531
91.77851.0235-0.46243.2459-0.56162.94280.068-0.0173-0.28370.3132-0.0822-0.19740.19510.17380.0142-0.37120.1302-0.1526-0.03160.0984-0.0301-45.094126.02794.244
102.64710.6685-2.02814.5171-0.61383.15540.08050.0206-0.0399-0.1421-0.0693-0.2102-0.0510.0684-0.0112-0.14120.1178-0.20150.03080.0418-0.1037-39.26336.0876-14.8167
111.8129-0.717-0.69333.8725-1.16353.55190.2150.1179-0.0104-0.602-0.2231-0.0899-0.41930.1050.0081-0.24230.0009-0.13340.0044-0.0557-0.0817-37.1318-21.7858-10.9778
122.1293-0.9826-0.2882.78120.51633.6335-0.1625-0.1721-0.03060.18450.0109-0.0649-0.23290.05380.1515-0.4715-0.1107-0.0854-0.0937-0.056-0.0462-40.169-36.295912.9081
132.2148-2.65041.2684.5135-1.06824.4189-0.2155-0.00330.12140.281-0.04840.1591-0.10180.0130.2639-0.2182-0.1210.0701-0.08770.0064-0.0913-45.8966-26.701638.9511
141.3620.30811.32267.291-0.29747.69070.03590.0890.03771.1310.00180.1587-0.47980.2038-0.03770.0375-0.04410.1777-0.00780.0237-0.1422-50.897-0.201547.2786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 191
2X-RAY DIFFRACTION2B15 - 191
3X-RAY DIFFRACTION3C15 - 191
4X-RAY DIFFRACTION4D15 - 191
5X-RAY DIFFRACTION5E15 - 193
6X-RAY DIFFRACTION6F15 - 191
7X-RAY DIFFRACTION7G15 - 191
8X-RAY DIFFRACTION8H15 - 191
9X-RAY DIFFRACTION9I15 - 191
10X-RAY DIFFRACTION10J15 - 191
11X-RAY DIFFRACTION11K15 - 191
12X-RAY DIFFRACTION12L15 - 193
13X-RAY DIFFRACTION13M15 - 191
14X-RAY DIFFRACTION14N15 - 191

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