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- PDB-3o1f: P1 crystal form of E. coli ClpS at 1.4 A resolution -

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Basic information

Entry
Database: PDB / ID: 3o1f
TitleP1 crystal form of E. coli ClpS at 1.4 A resolution
Components(ATP-dependent Clp protease adapter protein clpS) x 2
KeywordsHYDROLASE / adaptor
Function / homology
Function and homology information


molecular function inhibitor activity / protein catabolic process / peptidase activity / protein-folding chaperone binding / response to heat / proteolysis
Similarity search - Function
Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / ATP-dependent Clp protease adaptor protein ClpS / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal Protein L30; Chain: A, / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease adapter protein ClpS / ATP-dependent Clp protease adapter protein ClpS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRoman-Hernandez, G. / Hou, J.Y. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
CitationJournal: Mol.Cell / Year: 2011
Title: The ClpS Adaptor Mediates Staged Delivery of N-End Rule Substrates to the AAA+ ClpAP Protease.
Authors: Roman-Hernandez, G. / Hou, J.Y. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
History
DepositionJul 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease adapter protein clpS
B: ATP-dependent Clp protease adapter protein clpS


Theoretical massNumber of molelcules
Total (without water)18,5962
Polymers18,5962
Non-polymers00
Water7,242402
1
A: ATP-dependent Clp protease adapter protein clpS


Theoretical massNumber of molelcules
Total (without water)9,3061
Polymers9,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-dependent Clp protease adapter protein clpS


Theoretical massNumber of molelcules
Total (without water)9,2901
Polymers9,2901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.025, 28.051, 51.624
Angle α, β, γ (deg.)80.500, 77.880, 72.300
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ATP-dependent Clp protease adapter protein clpS


Mass: 9305.767 Da / Num. of mol.: 1 / Fragment: unp residues 26-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpS / Production host: Escherichia coli (E. coli) / References: UniProt: D3QP81, UniProt: P0A8Q6*PLUS
#2: Protein ATP-dependent Clp protease adapter protein clpS


Mass: 9289.767 Da / Num. of mol.: 1 / Fragment: unp residues 26-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpS / Production host: Escherichia coli (E. coli) / References: UniProt: D3QP81, UniProt: P0A8Q6*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Ammonium Formate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, pH 7, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 19, 2010 / Details: Varimax-HR
RadiationMonochromator: Varimax-HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 23654 / Num. obs: 23654 / % possible obs: 82.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.036 / Χ2: 1.003 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.453.10.159060.53132
1.45-1.513.50.119850.554168.3
1.51-1.583.70.07824840.614186.8
1.58-1.663.80.06425410.761187.7
1.66-1.763.80.05225460.752189.4
1.76-1.93.80.04825870.937190.5
1.9-2.093.80.04126261.151191.9
2.09-2.393.80.03527061.21193.6
2.39-3.023.80.03527411.524195.2
3.02-503.50.0325321.494188.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.4_129refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→22.488 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8593 / SU ML: 0.22 / σ(F): 2.03 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 1173 4.96 %
Rwork0.1734 --
obs0.1746 23635 82.54 %
all-23635 -
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.018 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 56.12 Å2 / Biso mean: 17.85 Å2 / Biso min: 6.72 Å2
Baniso -1Baniso -2Baniso -3
1-7.1254 Å2-1.1572 Å2-0.8587 Å2
2---2.3616 Å23.4085 Å2
3----4.7638 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 0 402 1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071340
X-RAY DIFFRACTIONf_angle_d1.1941815
X-RAY DIFFRACTIONf_chiral_restr0.07210
X-RAY DIFFRACTIONf_plane_restr0.009229
X-RAY DIFFRACTIONf_dihedral_angle_d17.242486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4001-1.46380.2104750.21671215129036
1.4638-1.5410.26191340.18762699283379
1.541-1.63750.20011680.17952980314887
1.6375-1.76390.19761570.17653044320189
1.7639-1.94130.19321760.17243064324090
1.9413-2.2220.17191400.1493164330493
2.222-2.79860.17831740.14793224339895
2.7986-22.49050.16871490.15223072322190

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