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

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Basic information

Entry
Database: PDB / ID: 5gkm
TitleCrystal structure of the N-terminal Domain of Caseinolytic protease associated chaperone ClpD from Arabidopsis thaliana
ComponentsAT5g51070/K3K7_27
KeywordsCHAPERONE / protease / Clp
Function / homology
Function and homology information


cellular response to heat / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
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 / ATPase family associated with various cellular activities (AAA) ...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 / 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
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMohapatra, C. / 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
DepositionJul 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AT5g51070/K3K7_27
B: AT5g51070/K3K7_27


Theoretical massNumber of molelcules
Total (without water)35,3282
Polymers35,3282
Non-polymers00
Water2,162120
1
A: AT5g51070/K3K7_27


Theoretical massNumber of molelcules
Total (without water)17,6641
Polymers17,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AT5g51070/K3K7_27


Theoretical massNumber of molelcules
Total (without water)17,6641
Polymers17,6641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.080, 37.310, 99.980
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 80 - 230 / Label seq-ID: 7 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein AT5g51070/K3K7_27 / AtClpD


Mass: 17663.988 Da / Num. of mol.: 2 / Fragment: UNP residues 79-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q94C10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20%(v/v) 2-propanol, 20%(w/v) PEG MME 2000, 100 mM MES monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 37033 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2 / CC1/2: 0.717 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOLREPphasing
Aimlessdata scaling
iMOSFLM7.1.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CTZ

5ctz
PDB Unreleased entry


Resolution: 1.6→35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.829 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1771 4.8 %RANDOM
Rwork0.196 ---
obs0.197 35497 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.05 Å2
2--0.34 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 0 120 2421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192348
X-RAY DIFFRACTIONr_bond_other_d0.0060.022229
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9593172
X-RAY DIFFRACTIONr_angle_other_deg0.88635159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7495305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45623.462104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34115427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1651520
X-RAY DIFFRACTIONr_chiral_restr0.1180.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022619
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02497
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_it1.5841.3731184
X-RAY DIFFRACTIONr_mcbond_other1.5791.3711183
X-RAY DIFFRACTIONr_mcangle_it2.0422.0481477
X-RAY DIFFRACTIONr_mcangle_other2.0412.0491478
X-RAY DIFFRACTIONr_scbond_it2.9611.6881164
X-RAY DIFFRACTIONr_scbond_other2.961.6891165
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0892.4061687
X-RAY DIFFRACTIONr_long_range_B_refined4.85116.9732765
X-RAY DIFFRACTIONr_long_range_B_other4.83516.9592762
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9166 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 143 -
Rwork0.268 2573 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1148-0.0774-0.33141.0578-0.33831.4626-0.05510.010.0035-0.02410.03160.0141-0.0222-0.05070.02350.0228-0.0164-0.00140.0184-0.00110.001110.133119.725162.3465
21.85340.2672-1.32670.9265-0.32993.4445-0.01610.0246-0.08180.02770.01890.0382-0.0542-0.1736-0.00280.02710.02250.02290.04980.01990.0228-3.70289.120288.174
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 373
2X-RAY DIFFRACTION2B80 - 331

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