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- PDB-1tg6: Crystallography and mutagenesis point to an essential role for th... -

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Basic information

Entry
Database: PDB / ID: 1tg6
TitleCrystallography and mutagenesis point to an essential role for the N-terminus of human mitochondrial ClpP
ComponentsPutative ATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / mitochondrial ClpP / Clp/Hsp 100 / ATP-dependent protease
Function / homology
Function and homology information


membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / 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 ...ClpP, Ser active site / Endopeptidase Clp serine active site. / 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
1,4-DIETHYLENE DIOXIDE / N-FORMYLMETHIONINE / ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKang, S.G. / Maurizi, M.R. / Thompson, M. / Mueser, T. / Ahvazi, B.
Citation
Journal: J.Struct.Biol. / Year: 2004
Title: Crystallography and mutagenesis point to an essential role for the N-terminus of human mitochondrial ClpP
Authors: Kang, S.G. / Maurizi, M.R. / Thompson, M. / Mueser, T. / Ahvazi, B.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Sequence and structure of ClpP, the proteolytic component of the ATP-dependent Clp protease of Escherichia Coli
Authors: Maurizi, M.R. / Clark, W.P. / Katayama, Y. / Rudikoff, S. / Pumphrey, J. / Bowers, B. / Gottesman, S.
History
DepositionMay 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 30, 2016Group: Other
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative ATP-dependent Clp protease proteolytic subunit
B: Putative ATP-dependent Clp protease proteolytic subunit
C: Putative ATP-dependent Clp protease proteolytic subunit
D: Putative ATP-dependent Clp protease proteolytic subunit
E: Putative ATP-dependent Clp protease proteolytic subunit
F: Putative ATP-dependent Clp protease proteolytic subunit
G: Putative ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,30934
Polymers211,4917
Non-polymers2,81827
Water13,926773
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29630 Å2
ΔGint-107 kcal/mol
Surface area51280 Å2
MethodPISA
2
A: Putative ATP-dependent Clp protease proteolytic subunit
B: Putative ATP-dependent Clp protease proteolytic subunit
C: Putative ATP-dependent Clp protease proteolytic subunit
D: Putative ATP-dependent Clp protease proteolytic subunit
E: Putative ATP-dependent Clp protease proteolytic subunit
F: Putative ATP-dependent Clp protease proteolytic subunit
G: Putative ATP-dependent Clp protease proteolytic subunit
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)428,61968
Polymers422,98214
Non-polymers5,63754
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area71360 Å2
ΔGint-229 kcal/mol
Surface area90450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.570, 119.002, 118.650
Angle α, β, γ (deg.)90, 130.159, 90
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 7 molecules ABCDEFG

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


Mass: 30213.020 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Plasmid: pVEX11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q16740, endopeptidase Clp

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Non-polymers , 5 types, 800 molecules

#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H11NO3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES pH 6.5, 10 % (V/V) dioxane, 10% glycerol, 1.5-1.8 M (NH4)2SO4 with 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X9B20.92
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATENov 4, 2000mirrors
ADSC QUANTUM 42CCDNov 4, 2000mirrors
RadiationMonochromator: SI(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.921
ReflectionResolution: 2.1→20 Å / Num. all: 338348 / Num. obs: 100429 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.17 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TYF

1tyf


Resolution: 2.1→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: NCS 7 fold averaging was employed during refinement
RfactorNum. reflectionSelection details
Rfree0.262 9091 RANDOM
Rwork0.224 --
all0.28 338348 -
obs0.308 100076 -
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.86 Å20 Å2-0.48 Å2
2--1.5 Å20 Å2
3----6.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10117 0 174 773 11064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.1→20 Å / Rfactor Rfree error: 0.003
RfactorNum. reflection% reflection
Rfree0.2628 9091 -
Rwork0.2243 --
obs-10076 9.1 %

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