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- PDB-6x60: ClpP2 from Chlamydia trachomatis with resolved handle loop -

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Basic information

Entry
Database: PDB / ID: 6x60
TitleClpP2 from Chlamydia trachomatis with resolved handle loop
ComponentsATP-dependent Clp protease proteolytic subunit 2
KeywordsHYDROLASE / Protease / Chlamydia trachomatis
Function / homology
Function and homology information


endopeptidase Clp complex / endopeptidase Clp / 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 2 / ATP-dependent Clp protease proteolytic subunit 2
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsAzadmanesh, J. / Struble, L.R. / Seleem, M.A. / Ouellette, S. / Conda-Sheridan, M. / Borgstahl, G.E.O.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P20GM121316-01A1 United States
Department of Defense (DOD, United States)PRMRP#PR172445 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)5P30CA036727-33 United States
CitationJournal: To Be Published
Title: ClpP2 from Chlamydia trachomatis with resolved handle loop
Authors: Azadmanesh, J. / Struble, L.R. / Borgstahl, G.E.O. / Ouellette, S. / Conda-Sheridan, M.
History
DepositionMay 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2


Theoretical massNumber of molelcules
Total (without water)154,5007
Polymers154,5007
Non-polymers00
Water0
1
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2

A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2


Theoretical massNumber of molelcules
Total (without water)309,00114
Polymers309,00114
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area53200 Å2
ΔGint-318 kcal/mol
Surface area84450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.710, 147.043, 97.059
Angle α, β, γ (deg.)90.000, 128.250, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 7 or resid 17 through 196))
21(chain B and (resid 3 through 7 or resid 17 through 196))
31(chain C and (resid 3 through 7 or resid 17 through 196))
41(chain D and (resid 3 through 7 or resid 17 through 196))
51(chain E and (resid 3 through 7 or resid 17 through 196))
61(chain F and (resid 3 through 7 or resid 17 through 196))
71(chain G and (resid 3 through 7 or resid 17 through 196))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVAL(chain A and (resid 3 through 7 or resid 17 through 196))AA3 - 73 - 7
12ALAALATHRTHR(chain A and (resid 3 through 7 or resid 17 through 196))AA17 - 19617 - 196
21LEULEUVALVAL(chain B and (resid 3 through 7 or resid 17 through 196))BB3 - 73 - 7
22ALAALATHRTHR(chain B and (resid 3 through 7 or resid 17 through 196))BB17 - 19617 - 196
31LEULEUVALVAL(chain C and (resid 3 through 7 or resid 17 through 196))CC3 - 73 - 7
32ALAALATHRTHR(chain C and (resid 3 through 7 or resid 17 through 196))CC17 - 19617 - 196
41LEULEUVALVAL(chain D and (resid 3 through 7 or resid 17 through 196))DD3 - 73 - 7
42ALAALATHRTHR(chain D and (resid 3 through 7 or resid 17 through 196))DD17 - 19617 - 196
51LEULEUVALVAL(chain E and (resid 3 through 7 or resid 17 through 196))EE3 - 73 - 7
52ALAALATHRTHR(chain E and (resid 3 through 7 or resid 17 through 196))EE17 - 19617 - 196
61LEULEUVALVAL(chain F and (resid 3 through 7 or resid 17 through 196))FF3 - 73 - 7
62ALAALATHRTHR(chain F and (resid 3 through 7 or resid 17 through 196))FF17 - 19617 - 196
71LEULEUVALVAL(chain G and (resid 3 through 7 or resid 17 through 196))GG3 - 73 - 7
72ALAALATHRTHR(chain G and (resid 3 through 7 or resid 17 through 196))GG17 - 19617 - 196

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 22071.467 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: clpP2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3KKY8, UniProt: O84712*PLUS, 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: Tacsimate pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 34843 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.096 / Net I/σ(I): 15.25
Reflection shellResolution: 2.8→2.87 Å / Mean I/σ(I) obs: 2.07 / Num. unique obs: 2318 / CC1/2: 0.699 / CC star: 0.907 / Rpim(I) all: 0.374 / Rrim(I) all: 0.712

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3794refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JCT

4jct


Resolution: 2.81→28.16 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 2029 6.03 %
Rwork0.1981 31603 -
obs0.2003 33632 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 286.23 Å2 / Biso mean: 49.5316 Å2 / Biso min: 20.94 Å2
Refinement stepCycle: final / Resolution: 2.81→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10106 0 0 0 10106
Num. residues----1328
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6170X-RAY DIFFRACTION20.391TORSIONAL
12B6170X-RAY DIFFRACTION20.391TORSIONAL
13C6170X-RAY DIFFRACTION20.391TORSIONAL
14D6170X-RAY DIFFRACTION20.391TORSIONAL
15E6170X-RAY DIFFRACTION20.391TORSIONAL
16F6170X-RAY DIFFRACTION20.391TORSIONAL
17G6170X-RAY DIFFRACTION20.391TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.81-2.880.38211070.3091516162365
2.88-2.950.33411230.25881999212285
2.95-3.040.31491470.25382295244298
3.04-3.140.29961470.252923252472100
3.14-3.250.29831510.25523352486100
3.25-3.380.26721500.222723322482100
3.38-3.530.23121460.215523512497100
3.53-3.720.23771600.190523142474100
3.72-3.950.2241440.192423492493100
3.95-4.260.2171510.163223532504100
4.26-4.680.16291500.14323392489100
4.68-5.360.2111540.1823512505100
5.36-6.730.24081440.209823542498100
6.73-28.160.19661550.173823902545100
Refinement TLS params.Method: refined / Origin x: -21.3601 Å / Origin y: 25.7384 Å / Origin z: 20.7137 Å
111213212223313233
T0.3053 Å2-0.0022 Å20.0683 Å2-0.2936 Å20.0182 Å2--0.2346 Å2
L0.4934 °20.0321 °20.2045 °2-0.257 °20.0214 °2--0.0033 °2
S-0.0084 Å °0.1584 Å °0.0463 Å °-0.0984 Å °0.0176 Å °-0.0713 Å °-0.0184 Å °0.0534 Å °-0.0097 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 197
2X-RAY DIFFRACTION1allB3 - 200
3X-RAY DIFFRACTION1allC3 - 199
4X-RAY DIFFRACTION1allD2 - 196
5X-RAY DIFFRACTION1allE3 - 203
6X-RAY DIFFRACTION1allF3 - 197
7X-RAY DIFFRACTION1allG3 - 200

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