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- PDB-4ryf: ClpP1/2 heterocomplex from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 4ryf
TitleClpP1/2 heterocomplex from Listeria monocytogenes
Components(ATP-dependent Clp protease proteolytic subunit) x 2
KeywordsHYDROLASE / Pathogenic bacteria / Enzyme catalysis / Proteolysis / Ser-protease / Heterocomplex / ClpP
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
MALONATE ION / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDahmen, M. / Vielberg, M.-T. / Groll, M. / Sieber, S.A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Structure and mechanism of the caseinolytic protease ClpP1/2 heterocomplex from Listeria monocytogenes.
Authors: Dahmen, M. / Vielberg, M.T. / Groll, M. / Sieber, S.A.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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

Downloads & links

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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
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,22835
Polymers316,19214
Non-polymers1,03621
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59280 Å2
ΔGint-343 kcal/mol
Surface area89630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.230, 127.150, 265.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.631688, -0.614401, -0.472737), (0.641634, 0.756599, -0.125953), (0.435058, -0.223761, 0.872155)-2.00653, -17.33913, -12.44223
3given(-0.205631, -0.740458, -0.639873), (0.832985, 0.210762, -0.511582), (0.513666, -0.638201, 0.573451)12.95146, -30.25041, -20.98034
4given(-0.8897, -0.286088, -0.355791), (0.425779, -0.23871, -0.872771), (0.164759, -0.927993, 0.334191)34.88639, -29.27438, -18.57713
5given(-0.896415, 0.418471, 0.146022), (-0.268407, -0.250372, -0.9302), (-0.352702, -0.873038, 0.336758)46.08775, -14.52639, -6.99402
6given(-0.222672, 0.832684, 0.507005), (-0.734935, 0.198321, -0.64849), (-0.640537, -0.517016, 0.567809)39.1497, 1.98869, 4.64116
7given(0.618852, 0.647814, 0.444251), (-0.620064, 0.750077, -0.230011), (-0.482227, -0.133121, 0.865873)18.81076, 9.16384, 8.02931

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp / ClpP1 subunit


Mass: 22701.615 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: clpP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y7Y1, endopeptidase Clp
#2: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp / ClpP2 subunit


Mass: 22468.670 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: clpP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RQI6, endopeptidase Clp
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Sodium-Malonate, 40% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2014
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 81904 / Num. obs: 78792 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.5 / % possible all: 98.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JCQ, 4JCT

4jcq

4jct


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 26.555 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21573 3941 5 %RANDOM
Rwork0.17962 ---
obs0.18144 74817 96.21 %-
all-78758 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.426 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--0.29 Å2-0 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19674 0 63 155 19892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01919975
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.96526978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02452512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95425.385910
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.353153658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.58115112
X-RAY DIFFRACTIONr_chiral_restr0.0660.23140
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114808
X-RAY DIFFRACTIONr_mcbond_it1.933.9910111
X-RAY DIFFRACTIONr_mcangle_it2.4735.96112602
X-RAY DIFFRACTIONr_scbond_it2.534.3049864
X-RAY DIFFRACTIONr_long_range_B_refined3.33332.99530031
X-RAY DIFFRACTIONr_rigid_bond_restr0.796319975
X-RAY DIFFRACTIONr_sphericity_free31.771576
X-RAY DIFFRACTIONr_sphericity_bonded20.632519816
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 292 -
Rwork0.286 5553 -
obs--98.22 %
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)
10.08970.1420.06550.83740.0680.1634-0.01840.0783-0.0433-0.05580.0274-0.0644-0.03410.0446-0.0090.0415-0.01590.01860.1078-0.0210.052554.45113.8131-53.7932
20.4430.1928-0.0380.2315-0.06740.1746-0.0240.0959-0.0467-0.03970.00150.00290.00110.00010.02250.0662-0.01270.0170.096-0.04540.028537.6016-1.9055-66.6525
30.42050.0757-0.3130.306-0.01470.315-0.0340.1061-0.0376-0.0297-0.00620.03320.0086-0.03550.04030.065-0.0233-0.01440.1267-0.04490.030811.2625-0.4995-67.858
40.24290.0056-0.00420.10990.19610.7066-0.0190.0868-0.0111-0.03270.00050.02620.0146-0.09230.01850.0357-0.0129-0.02920.0929-0.00480.0392-4.861516.8011-56.3341
50.24670.0104-0.0220.0518-0.00240.5048-0.00730.04760.0548-0.0037-0.0020.033-0.0362-0.05870.00940.03670.0045-0.01660.05090.00730.06431.442537.267-40.8347
60.4481-0.09780.2110.1626-0.03410.3244-0.01410.02410.0766-0.01860.00760.028-0.0598-0.00550.00650.048-0.0016-0.00230.03050.01440.067225.387945.2621-33.0525
70.3147-0.20670.04870.4728-0.14340.1387-0.00050.04620.0338-0.01320.0176-0.0223-0.01470.0228-0.01710.0411-0.01720.00250.05020.00530.052149.013934.7361-38.757
80.58850.2181-0.18790.393-0.11390.2997-0.02110.0153-0.13480.02160.02190.00320.07160.0473-0.00080.05420.00710.01320.0171-0.01510.108336.445-28.8913-28.7159
90.41130.1955-0.04140.6482-0.14990.286-0.007-0.0311-0.07460.00950.0037-0.00230.04680.00570.00330.02920.00460.00130.03740.00210.061251.8873-12.0116-15.0492
100.22280.0094-0.00690.4326-0.01330.15350.0018-0.0346-0.04880.01140.00650.00360.02930.001-0.00820.03870.0026-0.00320.05450.00190.043944.81358.9165-0.3441
110.3391-0.10990.12240.3887-0.10320.23830.0066-0.0374-0.03070.0293-0.00560.0040.0385-0.0003-0.00090.0402-00.00750.0589-0.00180.043220.251418.32084.5526
120.25170.03510.07670.2916-0.04660.4094-0.0003-0.0263-0.02060.0316-0.02240.00650.0444-0.01180.02280.0331-0.00670.01090.055-0.00280.0502-3.11758.8583-4.2276
130.26350.05790.09940.17790.07580.4335-0.00320.0084-0.07230.0182-0.0190.0270.01470.01890.02220.0447-0.00850.0180.0407-0.00170.0599-7.6634-12.1389-20.2028
140.2895-0.0289-0.01750.14340.09610.1673-0.02920.0356-0.1180.01590.02180.0030.0578-0.02350.00740.0551-0.02530.02580.0247-0.0170.09269.7785-29.0031-30.9926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 195
2X-RAY DIFFRACTION2B17 - 194
3X-RAY DIFFRACTION3C17 - 194
4X-RAY DIFFRACTION4D17 - 195
5X-RAY DIFFRACTION5E17 - 194
6X-RAY DIFFRACTION6F17 - 194
7X-RAY DIFFRACTION7G17 - 194
8X-RAY DIFFRACTION8H3 - 193
9X-RAY DIFFRACTION9I3 - 193
10X-RAY DIFFRACTION10J3 - 194
11X-RAY DIFFRACTION11K3 - 194
12X-RAY DIFFRACTION12L3 - 194
13X-RAY DIFFRACTION13M3 - 193
14X-RAY DIFFRACTION14N3 - 194

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