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- PDB-5gui: Crystal structure of the N-terminal Domain of Caseinolytic protea... -

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Basic information

Entry
Database: PDB / ID: 5gui
TitleCrystal structure of the N-terminal Domain of Caseinolytic protease associated chaperone ClpC1 from Arabidopsis thaliana
ComponentsChaperone protein ClpC1, chloroplastic
KeywordsCHAPERONE / ClpC / ClpC1
Function / homology
Function and homology information


Tic complex / plastid stroma / protein targeting to chloroplast / protein import into chloroplast stroma / regulation of chlorophyll biosynthetic process / chloroplast inner membrane / chloroplast organization / plant-type cell wall / chloroplast envelope / plastid ...Tic complex / plastid stroma / protein targeting to chloroplast / protein import into chloroplast stroma / regulation of chlorophyll biosynthetic process / chloroplast inner membrane / chloroplast organization / plant-type cell wall / chloroplast envelope / plastid / chloroplast stroma / ATP-dependent peptidase activity / chloroplast thylakoid membrane / chloroplast / mRNA binding / ATP hydrolysis activity / mitochondrion / ATP binding
Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain ...Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. / : / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Chaperone protein ClpC1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsJagdev, M.K. / Vasudevan, D.
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structures reveal N-terminal Domain of Arabidopsis thaliana ClpD to be highly divergent from that of ClpC1.
Authors: Mohapatra, C. / Kumar Jagdev, M. / Vasudevan, D.
History
DepositionAug 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 8, 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: Chaperone protein ClpC1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4546
Polymers16,9801
Non-polymers4755
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-14 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.100, 44.290, 97.560
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 Chaperone protein ClpC1, chloroplastic / ATP-dependent Clp protease ATP-binding subunit ClpC homolog 1 / Casein lytic proteinase C1 / ...ATP-dependent Clp protease ATP-binding subunit ClpC homolog 1 / Casein lytic proteinase C1 / Protein DE-REGULATED CAO ACCUMULATION 1 / Protein IRON-RESCUED MUTANT 1


Mass: 16979.635 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 94-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CLPC1 / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FI56
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M SODIUM CITRATE DEHYDRATE, 1.0M AMMONIUM PHOSPHATE MONOBASIC

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.2→17.54 Å / Num. obs: 54126 / % possible obs: 97.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.4
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.5 / % possible all: 98.4

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Processing

Software
NameVersionClassification
Aimlessdata reduction
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0107refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDC

3wdc


Resolution: 1.2→17.54 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.263 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 2742 5.1 %RANDOM
Rwork0.147 ---
obs-51310 97.9 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å20 Å2
2--0.5 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.2→17.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 25 130 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191371
X-RAY DIFFRACTIONr_bond_other_d0.0040.021414
X-RAY DIFFRACTIONr_angle_refined_deg1.9312.0021889
X-RAY DIFFRACTIONr_angle_other_deg1.03533266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2025197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9423.04369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89515281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2491519
X-RAY DIFFRACTIONr_chiral_restr0.1020.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021592
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02323
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1581.457651
X-RAY DIFFRACTIONr_mcbond_other2.1441.456650
X-RAY DIFFRACTIONr_mcangle_it2.6362.204827
X-RAY DIFFRACTIONr_mcangle_other2.642.206828
X-RAY DIFFRACTIONr_scbond_it3.2261.803720
X-RAY DIFFRACTIONr_scbond_other3.2621.812701
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8852.6041003
X-RAY DIFFRACTIONr_long_range_B_refined4.13813.0781698
X-RAY DIFFRACTIONr_long_range_B_other3.93412.341608
X-RAY DIFFRACTIONr_rigid_bond_restr3.07432785
X-RAY DIFFRACTIONr_sphericity_free34.721529
X-RAY DIFFRACTIONr_sphericity_bonded16.68852851
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 232 -
Rwork0.212 3801 -
obs--99.95 %

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