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- PDB-5g1r: Open conformation of Francisella tularensis ClpP at 1.9 A -

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Open data


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Basic information

Entry
Database: PDB / ID: 5g1r
TitleOpen conformation of Francisella tularensis ClpP at 1.9 A
ComponentsATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
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
ACETATE ION / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesFRANCISELLA TULARENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Mar 6, 2019Group: Advisory / Data collection / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
B: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
C: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
D: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
E: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
F: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
G: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,24719
Polymers155,2427
Non-polymers1,00412
Water19,5461085
1
A: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
B: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
C: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
D: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
E: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
F: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
G: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
hetero molecules

A: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
B: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
C: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
D: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
E: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
F: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
G: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,49338
Polymers310,48514
Non-polymers2,00824
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area70500 Å2
ΔGint-307.9 kcal/mol
Surface area90370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.942, 128.168, 98.260
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
ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT / ENDOPEPTIDASE CLP / 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
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1085 / 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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: RATIO 1:1, 293K, HANGING 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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.9→47.04 Å / Num. obs: 117661 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P2L

3p2l


Resolution: 1.9→98.26 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.562 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26937 5861 5 %RANDOM
Rwork0.20079 ---
obs0.20405 111731 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.142 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2---1.27 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→98.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10262 0 68 1085 11415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01910726
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210628
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.97914474
X-RAY DIFFRACTIONr_angle_other_deg1.041324450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10251332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88124.408490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.618151983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9521570
X-RAY DIFFRACTIONr_chiral_restr0.1150.21670
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211976
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022346
X-RAY DIFFRACTIONr_nbd_refined0.2530.26856
X-RAY DIFFRACTIONr_nbd_other0.1560.220684
X-RAY DIFFRACTIONr_nbtor_refined0.1790.210096
X-RAY DIFFRACTIONr_nbtor_other0.0790.211972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2630
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0430.212
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3510.2119
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.2192
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8411.9235320
X-RAY DIFFRACTIONr_mcbond_other1.8411.9215312
X-RAY DIFFRACTIONr_mcangle_it2.7212.866626
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1682.215406
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3413.2197840
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 417 -
Rwork0.278 8143 -
obs--99.96 %

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