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- PDB-4p15: Structure of the ClpC N-terminal domain from an alkaliphilic Baci... -

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Basic information

Entry
Database: PDB / ID: 4p15
TitleStructure of the ClpC N-terminal domain from an alkaliphilic Bacillus lehensis G1 species
ComponentsBacillus lehensis ClpC N-terminal domain
KeywordsHYDROLASE / Heat-shock protein / ClpC / Bacillus / alkalophilic
Function / homology
Function and homology information


ATP-dependent Clp protease ATP-binding subunit CLPT1/2 / Double Clp-N motif / Clp, N-terminal domain / Clp repeat (R) N-terminal domain / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bacillus lehensis ClpC N-terminal domain
Similarity search - Component
Biological speciesBacillus lehensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRashid, S.A. / Littler, D.R. / Illias, R.M. / Murad, A.M.A. / Rossjohn, J. / Beddoe, T. / Mahadi, N.M.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Malaysia Genome Institute Malaysia
CitationJournal: To Be Published
Title: Structure of the ClpC N-terminal domain at 1.85 Angstroms resolution from an alkaliphilic Bacillus lehensis G1 species
Authors: Rashid, S.A. / Littler, D.R.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacillus lehensis ClpC N-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0833
Polymers15,8911
Non-polymers1922
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-29 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.620, 84.620, 32.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Bacillus lehensis ClpC N-terminal domain


Mass: 15891.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus lehensis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A087WNH8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.22 Å3/Da / Density % sol: 44.49 % / Description: Hexagonal crystal
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Protein crystallization was carried out using the hanging-drop vapor-diffusion method using 24-well Limbro tissue culture plates (ICN Inc.) at 19C. Drops were formed by mixing equal volumes ...Details: Protein crystallization was carried out using the hanging-drop vapor-diffusion method using 24-well Limbro tissue culture plates (ICN Inc.) at 19C. Drops were formed by mixing equal volumes (1 ul) of protein solution at 50 mg/mL and the reservoir solution containing 0.1M phosphate-citrate pH 4.2 20% polyethylene glycol 1000, 0.2M lithium sulphate. Hexagonal crystals appeared after 20-30 days

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 6, 2012 / Details: Osmic focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→73.29 Å / Num. all: 11473 / Num. obs: 11473 / % possible obs: 99.6 % / Redundancy: 6.85 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.6
Reflection shellResolution: 1.85→73.29 Å / Redundancy: 6.85 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 19.6 / % possible all: 99.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→36.641 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 547 4.79 %RANDOM
Rwork0.21 ---
obs0.2114 11416 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: 1 / Resolution: 1.85→36.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 10 12 1070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061081
X-RAY DIFFRACTIONf_angle_d0.9551452
X-RAY DIFFRACTIONf_dihedral_angle_d15.646415
X-RAY DIFFRACTIONf_chiral_restr0.065166
X-RAY DIFFRACTIONf_plane_restr0.003188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-2.03620.30061230.2472666X-RAY DIFFRACTION98
2.0362-2.33080.27311440.2092701X-RAY DIFFRACTION100
2.3308-2.93640.24411450.21712718X-RAY DIFFRACTION100
2.9364-36.64860.21881350.20052784X-RAY DIFFRACTION100

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