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- PDB-7d34: AtClpS1-peptide complex -

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Basic information

Entry
Database: PDB / ID: 7d34
TitleAtClpS1-peptide complex
ComponentsATP-dependent Clp protease adapter protein CLPS1, chloroplastic
KeywordsPEPTIDE BINDING PROTEIN / Arabidopsis thaliana / ClpS / N-degron pathway / complex structure
Function / homology
Function and homology information


positive regulation of proteolysis involved in protein catabolic process / chloroplast stroma / protein catabolic process / peptidase activity / protein-macromolecule adaptor activity / proteolysis
Similarity search - Function
ATP-dependent Clp protease adaptor protein ClpS / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like
Similarity search - Domain/homology
ACETIC ACID / ALANINE / PHENYLALANINE / ATP-dependent Clp protease adapter protein CLPS1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsHeo, J. / Kim, L. / Kwon, D.H. / Song, H.K.
CitationJournal: Protein Sci. / Year: 2021
Title: Structural basis for the N-degron specificity of ClpS1 from Arabidopsis thaliana.
Authors: Kim, L. / Heo, J. / Kwon, D.H. / Shin, J.S. / Jang, S.H. / Park, Z.Y. / Song, H.K.
History
DepositionSep 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: ATP-dependent Clp protease adapter protein CLPS1, chloroplastic
B: ATP-dependent Clp protease adapter protein CLPS1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1055
Polymers17,7912
Non-polymers3143
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint1 kcal/mol
Surface area8150 Å2
Unit cell
Length a, b, c (Å)81.056, 38.005, 61.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ATP-dependent Clp protease adapter protein CLPS1, chloroplastic


Mass: 8895.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CPLS1, CLPT, At1g68660, F24J5.10, F24J5.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SX29
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate pH 4.6 (Hampton Research, HR2-731), 2 M NaCl (Hampton Research, HR2-637)

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13209 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rpim(I) all: 0.028 / Net I/σ(I): 48.8
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 632 / Rpim(I) all: 0.168

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O2X

4o2x


Resolution: 2.007→34.41 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 0 / Phase error: 31.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2987 1292 9.97 %
Rwork0.2744 --
obs0.2769 12954 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.007→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 20 12 1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091245
X-RAY DIFFRACTIONf_angle_d1.0251689
X-RAY DIFFRACTIONf_dihedral_angle_d15.377759
X-RAY DIFFRACTIONf_chiral_restr0.054198
X-RAY DIFFRACTIONf_plane_restr0.006225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0071-2.08750.37171340.31691196X-RAY DIFFRACTION93
2.0875-2.18250.35871370.33731270X-RAY DIFFRACTION97
2.1825-2.29750.37421350.32981209X-RAY DIFFRACTION94
2.2975-2.44140.34461420.31021292X-RAY DIFFRACTION99
2.4414-2.62980.34221430.30961302X-RAY DIFFRACTION99
2.6298-2.89440.3421470.311318X-RAY DIFFRACTION99
2.8944-3.31290.31721470.29491321X-RAY DIFFRACTION100
3.3129-4.17280.29031480.24281323X-RAY DIFFRACTION98
4.1728-34.410.22811590.22811431X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.5346 Å / Origin y: 4.0995 Å / Origin z: 14.6048 Å
111213212223313233
T0.2672 Å2-0.0143 Å2-0.0868 Å2-0.2581 Å20.0095 Å2--0.2271 Å2
L3.9617 °20.8158 °2-0.2327 °2-0.5582 °20.0385 °2--1.2202 °2
S0.0944 Å °-0.6675 Å °-0.1064 Å °0.1448 Å °-0.0807 Å °-0.0629 Å °0.0144 Å °-0.086 Å °-0.0099 Å °
Refinement TLS groupSelection details: all

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