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- PDB-5g1q: Compressed conformation of Francisella tularensis ClpP at 2.84 A -

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Basic information

Entry
Database: PDB / ID: 5g1q
TitleCompressed conformation of Francisella tularensis ClpP at 2.84 A
ComponentsCLP PROTEASE PROTEOLYTIC SUBUNIT P
KeywordsHYDROLASE
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesFRANCISELLA TULARENSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsDiaz-Saez, L. / Hunter, W.N.
CitationJournal: Proteins / Year: 2017
Title: Open and compressed conformations of Francisella tularensis ClpP.
Authors: Diaz-Saez, L. / Pankov, G. / Hunter, W.N.
History
DepositionMar 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLP PROTEASE PROTEOLYTIC SUBUNIT P
B: CLP PROTEASE PROTEOLYTIC SUBUNIT P
C: CLP PROTEASE PROTEOLYTIC SUBUNIT P
D: CLP PROTEASE PROTEOLYTIC SUBUNIT P
E: CLP PROTEASE PROTEOLYTIC SUBUNIT P
F: CLP PROTEASE PROTEOLYTIC SUBUNIT P
G: CLP PROTEASE PROTEOLYTIC SUBUNIT P


Theoretical massNumber of molelcules
Total (without water)155,2427
Polymers155,2427
Non-polymers00
Water00
1
A: CLP PROTEASE PROTEOLYTIC SUBUNIT P
B: CLP PROTEASE PROTEOLYTIC SUBUNIT P
C: CLP PROTEASE PROTEOLYTIC SUBUNIT P
D: CLP PROTEASE PROTEOLYTIC SUBUNIT P
E: CLP PROTEASE PROTEOLYTIC SUBUNIT P
F: CLP PROTEASE PROTEOLYTIC SUBUNIT P
G: CLP PROTEASE PROTEOLYTIC SUBUNIT P

A: CLP PROTEASE PROTEOLYTIC SUBUNIT P
B: CLP PROTEASE PROTEOLYTIC SUBUNIT P
C: CLP PROTEASE PROTEOLYTIC SUBUNIT P
D: CLP PROTEASE PROTEOLYTIC SUBUNIT P
E: CLP PROTEASE PROTEOLYTIC SUBUNIT P
F: CLP PROTEASE PROTEOLYTIC SUBUNIT P
G: CLP PROTEASE PROTEOLYTIC SUBUNIT P


Theoretical massNumber of molelcules
Total (without water)310,48514
Polymers310,48514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area45430 Å2
ΔGint-286.9 kcal/mol
Surface area87390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.461, 125.940, 96.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
CLP PROTEASE PROTEOLYTIC SUBUNIT P


Mass: 22177.490 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FRANCISELLA TULARENSIS (bacteria) / Plasmid: MODIFIED PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q5NH47, endopeptidase Clp

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: RATIO 1:1, 293K, SITTING DROP. RESERVOIR CONDITION: 0.2 M NACL, 30% (V/V) MPD AND 0.1 M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.84→96.95 Å / Num. obs: 32741 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.9
Reflection shellResolution: 2.84→2.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P2L

3p2l


Resolution: 2.84→96.95 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.8 / SU B: 22.175 / SU ML: 0.428 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGION IN EVERY SUBUNIT FROM ABOUT RESIDUE 129 TO 162.
RfactorNum. reflection% reflectionSelection details
Rfree0.32604 1635 5 %RANDOM
Rwork0.24859 ---
obs0.25239 31087 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.592 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20 Å2
2--1.28 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.84→96.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9309 0 0 0 9309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199468
X-RAY DIFFRACTIONr_bond_other_d0.0020.029166
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.97412793
X-RAY DIFFRACTIONr_angle_other_deg0.914321074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28851197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20224.988411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.957151650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5121542
X-RAY DIFFRACTIONr_chiral_restr0.0680.21489
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022022
X-RAY DIFFRACTIONr_nbd_refined0.1690.23950
X-RAY DIFFRACTIONr_nbd_other0.1350.218460
X-RAY DIFFRACTIONr_nbtor_refined0.1580.28978
X-RAY DIFFRACTIONr_nbtor_other0.0720.29960
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2484
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3323.6694848
X-RAY DIFFRACTIONr_mcbond_other1.3313.6694847
X-RAY DIFFRACTIONr_mcangle_it2.3775.4836025
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9893.7894620
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8175.6476768
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.836→2.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 140 -
Rwork0.316 2238 -
obs--98.02 %

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