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- PDB-6pbu: ClpP1 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 6pbu
TitleClpP1 from Mycobacterium smegmatis
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Protease / Degradation / AAA+ unfoldase
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / serine-type endopeptidase activity / proteolysis / 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
MALONATE ION / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHeras, B. / Nagpal, J. / Dougan, D.A.
CitationJournal: Sci Rep / Year: 2019
Title: Molecular and structural insights into an asymmetric proteolytic complex (ClpP1P2) from Mycobacterium smegmatis.
Authors: Nagpal, J. / Paxman, J.J. / Zammit, J.E. / Alhuwaider, A. / Truscott, K.N. / Heras, B. / Dougan, D.A.
History
DepositionJun 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,21216
Polymers164,2947
Non-polymers9189
Water19,5101083
1
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
hetero molecules

A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,42532
Polymers328,58814
Non-polymers1,83718
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area55830 Å2
ΔGint-299 kcal/mol
Surface area85080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.617, 169.617, 114.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 23470.572 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: clpP, MSMEG_4673 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0R198, endopeptidase Clp
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1083 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2.1 - 3.4 M sodium malonate pH 6.6 - 6.8 / PH range: 6.6 - 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 111562 / % possible obs: 99.7 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.035 / Rrim(I) all: 0.127 / Χ2: 1.515 / Net I/σ(I): 8.5 / Num. measured all: 1387039
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.03111.18154120.8130.3641.2381.40198.3
2.03-2.0711.11.00554510.8480.3091.0521.40498.8
2.07-2.1111.10.8654840.8850.2640.9011.43199.1
2.11-2.1511.20.73454870.9160.2240.7681.45999.3
2.15-2.211.40.6255070.9350.1880.6481.4699.4
2.2-2.2511.50.53554890.9550.1620.5591.49799.8
2.25-2.3111.60.50155490.9590.1510.5241.51999.9
2.31-2.3711.80.42355600.9680.1260.4421.51499.9
2.37-2.44120.36855200.980.1090.3841.535100
2.44-2.5212.20.30655590.9840.090.3191.552100
2.52-2.6112.50.28755670.9850.0840.31.558100
2.61-2.7112.70.2255580.9910.0640.2291.55199.9
2.71-2.84130.1955890.9930.0540.1971.55599.9
2.84-2.9913.20.14855760.9950.0420.1541.6100
2.99-3.1713.30.12455850.9960.0350.1291.76100
3.17-3.4213.30.10856240.9970.030.1121.884100
3.42-3.7613.30.08856510.9980.0250.0911.874100
3.76-4.3113.80.06556710.9990.0180.0671.522100
4.31-5.43140.04657360.9990.0130.0481.187100
5.43-5014.10.035598710.010.0361.04699.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CBY

2cby


Resolution: 2→37.149 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2146 5584 5.02 %
Rwork0.1777 --
obs0.1795 111313 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.24 Å2 / Biso mean: 31.2464 Å2 / Biso min: 13.42 Å2
Refinement stepCycle: final / Resolution: 2→37.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10121 0 63 1087 11271
Biso mean--51.41 39.8 -
Num. residues----1336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0004-2.02310.26081580.2323190334891
2.0231-2.04690.25031960.22543468366498
2.0469-2.07180.27171880.21773435362399
2.0718-2.09810.25821850.21183447363299
2.0981-2.12570.26451770.2123483366099
2.1257-2.15480.27251750.20873522369799
2.1548-2.18560.26531570.20953476363399
2.1856-2.21820.25622040.201934813685100
2.2182-2.25280.2551910.192735033694100
2.2528-2.28980.25031800.197335253705100
2.2898-2.32930.23281850.20235173702100
2.3293-2.37160.24491910.198135103701100
2.3716-2.41720.27131820.19635083690100
2.4172-2.46650.22181720.195835233695100
2.4665-2.52020.22871880.195135083696100
2.5202-2.57880.27311750.204735533728100
2.5788-2.64320.25162090.200134773686100
2.6432-2.71470.23611780.194335523730100
2.7147-2.79450.23362060.207435173723100
2.7945-2.88470.21562010.191335243725100
2.8847-2.98780.22111850.188335283713100
2.9878-3.10730.2272120.178335203732100
3.1073-3.24870.24491520.18073584373699
3.2487-3.41980.19451920.16973538373099
3.4198-3.63390.17471830.158335633746100
3.6339-3.91420.17971940.147335683762100
3.9142-4.30760.17731870.129635903777100
4.3076-4.92970.14241840.134236283812100
4.9297-6.20620.20421850.180936753860100
6.2062-37.1550.21322120.17693816402899

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