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- PDB-1r6b: High resolution crystal structure of ClpA -

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Basic information

Entry
Database: PDB / ID: 1r6b
TitleHigh resolution crystal structure of ClpA
ComponentsClpA protein
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 / Helicase, Ruva Protein; domain 3 - #60 / 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 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent Clp protease ATP-binding subunit ClpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å
AuthorsXia, D. / Maurizi, M.R. / Guo, F. / Singh, S.K. / Esser, L.
Citation
Journal: 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.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease
Authors: Guo, F. / Maurizi, M.R. / Esser, L. / Xia, D.
History
DepositionOct 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE THE AUTHORS BELIEVE THAT Their sequence is CORRECT SINCE IT IS based on the new sequence ...SEQUENCE THE AUTHORS BELIEVE THAT Their sequence is CORRECT SINCE IT IS based on the new sequence standard on the total E. coli genome.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: ClpA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2316
Polymers84,3041
Non-polymers9275
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.110, 124.110, 97.049
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 ClpA protein


Mass: 84303.812 Da / Num. of mol.: 1 / Mutation: M169L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pSK39 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABH9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: hepes, potassium chloride, magnesium chloride, isopropanol, PEG 4000, glycerol, ADP, pH 7.5, VAPOR DIFFUSION, 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
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 37627 / Num. obs: 37627 / % possible obs: 0.931 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 2.7 % / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 21.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 1.36 / Num. unique all: 3170 / Rsym value: 0.303 / % possible all: 0.79

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.502 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.34 / ESU R Free: 0.252 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27784 773 2.1 %RANDOM
Rwork0.23415 ---
obs0.23504 36841 93.85 %-
all-37627 --
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: 59.217 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0.52 Å20 Å2
2---1.05 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 0 57 60 5623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0215644
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9737630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3053700
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.332151056
X-RAY DIFFRACTIONr_chiral_restr0.2540.2880
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024186
X-RAY DIFFRACTIONr_nbd_refined0.1920.32499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.5266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.397
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.515
X-RAY DIFFRACTIONr_mcbond_it1.3490.83492
X-RAY DIFFRACTIONr_mcangle_it3.2923.85620
X-RAY DIFFRACTIONr_scbond_it5.44932152
X-RAY DIFFRACTIONr_scangle_it7.6664.52010
LS refinement shellResolution: 2.25→2.312 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.417 43
Rwork0.367 2314
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)
16.97181.2381-1.63645.5416-1.44524.3035-0.0667-0.0659-0.30980.12880.38750.87630.0907-0.9351-0.32080.0862-0.1157-0.01370.32240.24180.3052142.158760.66746.5814
29.4971-2.4229-0.73736.59460.72655.7640.21380.6213-1.3844-0.8327-0.16980.54280.8155-0.1503-0.0440.38910.02-0.14840.32820.010.2247141.80520.411715.6413
36.1455-0.3362-0.21366.2689-0.25449.3186-0.16550.14210.4435-0.06270.15510.2738-0.5998-0.11270.01040.1082-0.03520.04450.02430.0050.048120.093943.630816.8127
46.17651.04871.40874.8539-0.11445.0799-0.0783-0.0010.23540.0235-0.1233-0.3037-0.09690.34450.20160.33640.0108-0.16410.0998-0.08960.1608100.540213.66434.6731
56.67620.28832.18783.75491.04037.43650.5662-0.1655-0.7680.4447-0.21930.17020.8782-0.2917-0.34690.0814-0.0137-0.01380.04290.01710.232674.2875-6.111125.506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA1 - 1411 - 141
2X-RAY DIFFRACTION2XA169 - 349169 - 349
3X-RAY DIFFRACTION3XA350 - 438350 - 438
4X-RAY DIFFRACTION4XA439 - 653439 - 653
5X-RAY DIFFRACTION5XA654 - 751654 - 751

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