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- PDB-1r6c: High resolution structure of ClpN -

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Basic information

Entry
Database: PDB / ID: 1r6c
TitleHigh resolution structure of ClpN
ComponentsATP-dependent Clp protease ATP-binding subunit clpA
KeywordsHYDROLASE / ClpA / AAA+ / N-terminal Domain / ClpS / crystal / binding mechanism
Function / homology
Function and homology information


endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / cellular response to heat / response to oxidative stress / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / 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 ...Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / 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 profile. / Clp, repeat (R) domain / 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
ATP-dependent Clp protease ATP-binding subunit ClpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.15 Å
AuthorsXia, D. / Maurizi, M.R. / Guo, F. / Singh, S.K. / Esser, L.
CitationJournal: J.Struct.Biol. / Year: 2004
Title: Crystallographic investigation of peptide binding sites in the N-domain of the ClpA chaperone
Authors: Xia, D. / Esser, L. / Singh, S.K. / Guo, F. / Maurizi, M.R.
History
DepositionOct 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
X: ATP-dependent Clp protease ATP-binding subunit clpA


Theoretical massNumber of molelcules
Total (without water)16,2001
Polymers16,2001
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.040, 51.990, 65.133
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 ATP-binding subunit clpA


Mass: 16200.268 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CLPA, LOPD, B0882, C1019, Z1119, ECS0968 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABH9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.88 Å3/Da / Density % sol: 34.69 %
Crystal growTemperature: 294 K / Method: hanging drop
Details: 0.02M HEPES at pH 7.4 (protein solution) mixed 1:1 with 0.1M PIPES at pH 7.0, 35% (w/v) PEG 8000, 0.32M sodium citrate, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 6243 / Num. obs: 6243 / % possible obs: 0.88 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Net I/σ(I): 51.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 27.48 / Num. unique all: 511 / Rsym value: 0.052 / % possible all: 0.744

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.873 / SU B: 4.859 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.382 / ESU R Free: 0.247 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24326 241 3.9 %RANDOM
Rwork0.16748 ---
all-5979 --
obs-5979 88.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.105 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1126 0 0 70 1196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211142
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7591.9491546
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2263141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30215204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02872
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.3511
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.575
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.351
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.590.8711
X-RAY DIFFRACTIONr_mcangle_it3.7313.81143
X-RAY DIFFRACTIONr_scbond_it6.4463431
X-RAY DIFFRACTIONr_scangle_it9.54.5403
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 13
Rwork0.18 353
Refinement TLS params.Method: refined / Origin x: 44.4944 Å / Origin y: 12.302 Å / Origin z: 174.6293 Å
111213212223313233
T0.0289 Å2-0.0093 Å20.0054 Å2-0.045 Å2-0.0156 Å2--0.0056 Å2
L3.4574 °20.4572 °2-0.1336 °2-4.1204 °2-0.3817 °2--2.84 °2
S-0.1 Å °-0.0011 Å °-0.0071 Å °-0.0237 Å °0.1186 Å °-0.1152 Å °-0.022 Å °0.0972 Å °-0.0186 Å °

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