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- PDB-9irp: Structure of ClpP from Staphylococcus aureus in complex with ZG297 -

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Basic information

Entry
Database: PDB / ID: 9irp
TitleStructure of ClpP from Staphylococcus aureus in complex with ZG297
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / ClpP / Staphylococcus aureus / activator / protease
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 / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
: / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsWei, B.Y. / Wang, P.Y. / Zhang, T. / Yang, C.-G.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22037007 China
National Natural Science Foundation of China (NSFC)22107109 China
National Natural Science Foundation of China (NSFC)22307029 China
CitationJournal: Cell Rep Med / Year: 2024
Title: Structure-guided development of selective caseinolytic protease P agonists as antistaphylococcal agents.
Authors: Zhang, T. / Wang, P. / Zhou, H. / Wei, B. / Zhao, Y. / Li, J. / Zhang, M. / Wu, W. / Lan, L. / Gan, J. / Yang, C.G.
History
DepositionJul 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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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)321,36840
Polymers313,11614
Non-polymers8,25226
Water35,3631963
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55770 Å2
ΔGint-296 kcal/mol
Surface area93690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.581, 190.320, 96.401
Angle α, β, γ (deg.)90.00, 117.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 22365.414 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: clpP_1, clpP, clpP_2, A6760_03845, BN1321_180012, CV021_05845, E1948_01285, E1948_03940, EP54_12650, EQ90_03850, FAF17_09860, G6W63_01780, G6Y24_04455, GO793_13920, GO814_03290, GO942_03115, ...Gene: clpP_1, clpP, clpP_2, A6760_03845, BN1321_180012, CV021_05845, E1948_01285, E1948_03940, EP54_12650, EQ90_03850, FAF17_09860, G6W63_01780, G6Y24_04455, GO793_13920, GO814_03290, GO942_03115, GQX37_00485, GZ156_04030, GZ163_03895, H2639_09715, HMPREF3211_00508, M1K003_1188, NCTC10702_01301, NCTC13131_00808, NCTC5664_02933, NCTC7878_03438, NCTC7972_01134, QU38_10910, SAMEA1531744_00638, SAMEA2078260_01084, SAMEA2078588_00822, SAMEA2080344_01058, SAMEA2081063_00578, SAMEA4008575_00328, SAMEA70146418_00708, SAMEA70153168_02138, SAMEA70245418_01774
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1I3W4, endopeptidase Clp
#2: Chemical
ChemComp-Z53 / (6S,9aS)-6-[(2S)-butan-2-yl]-4,7-bis(oxidanylidene)-8-(phenanthren-9-ylmethyl)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide / 2-(4-(3-tert-butyl-5-(3-thiazol-2-ylureido)-1H-pyrazol-1-yl)phenyl)acetic acid


Mass: 568.630 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C31H35F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1963 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 30% v/v (+/-)-2-methyl-2,4-pentanediol, 0.1 M sodium acetate trihydrate (pH 4.6), 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.988 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 228483 / % possible obs: 97.1 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.093 / Χ2: 0.038 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.973.40.442216251.011192
1.97-2.053.60.272222370.482194.7
2.05-2.1440.32223541.047195.2
2.14-2.254.50.275227571.043197
2.25-2.394.60.164229730.766197.6
2.39-2.584.80.135229980.863197.9
2.58-2.845.40.119233201.066199
2.84-3.255.60.088232381.048198.8
3.25-4.096.40.075234931.214199.5
4.09-306.60.056234880.822199

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXv1.0refinement
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→29.859 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 10728 5.06 %
Rwork0.1731 --
obs0.1749 211948 89.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→29.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20066 0 586 1963 22615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820959
X-RAY DIFFRACTIONf_angle_d1.10928405
X-RAY DIFFRACTIONf_dihedral_angle_d10.51612717
X-RAY DIFFRACTIONf_chiral_restr0.0623282
X-RAY DIFFRACTIONf_plane_restr0.0073691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9013-1.92290.29631600.24252674X-RAY DIFFRACTION36
1.9229-1.94550.2811900.2153700X-RAY DIFFRACTION50
1.9455-1.96920.2473060.22084505X-RAY DIFFRACTION61
1.9692-1.99410.263260.21895177X-RAY DIFFRACTION71
1.9941-2.02030.26722760.2185711X-RAY DIFFRACTION76
2.0203-2.0480.2683890.21315863X-RAY DIFFRACTION80
2.048-2.07730.28423360.22755951X-RAY DIFFRACTION81
2.0773-2.10830.2414010.20396696X-RAY DIFFRACTION90
2.1083-2.14120.24963890.19726955X-RAY DIFFRACTION94
2.1412-2.17630.25393210.18667076X-RAY DIFFRACTION95
2.1763-2.21380.22613570.17997164X-RAY DIFFRACTION96
2.2138-2.25410.24653350.19467151X-RAY DIFFRACTION95
2.2541-2.29740.22283840.18087240X-RAY DIFFRACTION96
2.2974-2.34430.22433500.17977295X-RAY DIFFRACTION98
2.3443-2.39520.21713830.18167296X-RAY DIFFRACTION98
2.3952-2.45090.24653550.18067271X-RAY DIFFRACTION98
2.4509-2.51220.21684170.17317242X-RAY DIFFRACTION97
2.5122-2.58010.21444090.17297315X-RAY DIFFRACTION99
2.5801-2.65590.19553690.17037399X-RAY DIFFRACTION99
2.6559-2.74160.21733860.17637385X-RAY DIFFRACTION99
2.7416-2.83950.20263800.1747415X-RAY DIFFRACTION99
2.8395-2.95310.2084030.17057384X-RAY DIFFRACTION99
2.9531-3.08740.20084430.17347363X-RAY DIFFRACTION99
3.0874-3.250.20584030.17047269X-RAY DIFFRACTION98
3.25-3.45330.19634100.177410X-RAY DIFFRACTION99
3.4533-3.71950.18793260.15777503X-RAY DIFFRACTION99
3.7195-4.0930.19053310.1567527X-RAY DIFFRACTION100
4.093-4.68330.16834190.13867339X-RAY DIFFRACTION99
4.6833-5.8930.18053790.15987479X-RAY DIFFRACTION99
5.893-29.8590.15483950.15487465X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.5992 Å / Origin y: -30.6259 Å / Origin z: 26.9134 Å
111213212223313233
T0.0501 Å20.0075 Å2-0.0392 Å2-0.0659 Å20.0567 Å2---0.0144 Å2
L0.4226 °20.0835 °2-0.1347 °2-0.4914 °2-0.0143 °2--0.1834 °2
S-0.0082 Å °-0.0852 Å °-0.1027 Å °0.0441 Å °-0.0238 Å °-0.0723 Å °-0.0233 Å °0.0352 Å °0.0063 Å °
Refinement TLS groupSelection details: all

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