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- PDB-2zl2: Crystal structure of H.pylori ClpP in complex with the peptide NVLGFTQ -

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Basic information

Entry
Database: PDB / ID: 2zl2
TitleCrystal structure of H.pylori ClpP in complex with the peptide NVLGFTQ
Components
  • A peptide substrate-NVLGFTQ
  • A peptide substrate-NVLGFTQ for Chain R and S
  • ATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Peptide substrate / Cytoplasm / Protease / Serine 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 / cytoplasm
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
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, D.Y. / Kim, K.K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The structural basis for the activation and peptide recognition of bacterial ClpP
Authors: Kim, D.Y. / Kim, K.K.
History
DepositionApr 2, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
O: A peptide substrate-NVLGFTQ
P: A peptide substrate-NVLGFTQ
Q: A peptide substrate-NVLGFTQ
R: A peptide substrate-NVLGFTQ for Chain R and S
S: A peptide substrate-NVLGFTQ for Chain R and S
T: A peptide substrate-NVLGFTQ
U: A peptide substrate-NVLGFTQ
V: A peptide substrate-NVLGFTQ
W: A peptide substrate-NVLGFTQ
X: A peptide substrate-NVLGFTQ


Theoretical massNumber of molelcules
Total (without water)309,11824
Polymers309,11824
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50570 Å2
ΔGint-246.8 kcal/mol
Surface area85290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.741, 166.425, 187.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21547.674 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: clpP / Plasmid: pET_22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P56156, endopeptidase Clp
#2: Protein/peptide
A peptide substrate-NVLGFTQ


Mass: 777.865 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Protein/peptide A peptide substrate-NVLGFTQ for Chain R and S


Mass: 613.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
Sequence detailsBECAUSE THE ELECTRON DENSITIES FOR ALL OF SIDE CHAINS IN CHAIN R AND S WERE POOR, THE AUTHORS WERE ...BECAUSE THE ELECTRON DENSITIES FOR ALL OF SIDE CHAINS IN CHAIN R AND S WERE POOR, THE AUTHORS WERE UNABLE TO ASSIGN SIDE CHAINS OF THEM. IN ADDITION, RESIDUE NUMBERS ARE ARBITRARY. THE FOLLOWING IS THE ONE-LETTER SEQUENCE FOR THE PROTEIN IN CHAIN R AND S MODELED IN THIS STRUCTURE, NVLGFTQ.

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: 32% PEG 400, 0.1M HEPES, 0.35M magnesium chloride, pH 7.5, Microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 100644 / Biso Wilson estimate: 49.6 Å2

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZL0

2zl0


Resolution: 2.5→19.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4793989.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 10067 10 %RANDOM
Rwork0.23 ---
obs0.23 100479 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.4273 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 46.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å20 Å2
2---2.9 Å20 Å2
3----1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18687 0 0 0 18687
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 1694 10.2 %
Rwork0.291 14889 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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