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- PDB-7dft: Crystal structure of Xanthomonas oryzae ClpP -

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Basic information

Entry
Database: PDB / ID: 7dft
TitleCrystal structure of Xanthomonas oryzae ClpP
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Caseinolytic protease P / Clp protease
Function / homology
Function and homology information


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 speciesXanthomonas oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYang, C.-G. / Yang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22037007 China
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Dysregulation of ClpP by Small-Molecule Activators Used Against Xanthomonas oryzae pv. oryzae Infections.
Authors: Yang, T. / Zhang, T. / Zhou, X. / Wang, P. / Gan, J. / Song, B. / Yang, S. / Yang, C.G.
History
DepositionNov 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: 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
Revision 1.2Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,02415
Polymers159,7417
Non-polymers2848
Water17,204955
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20820 Å2
ΔGint-184 kcal/mol
Surface area48930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.548, 132.548, 187.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11G-516-

HOH

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Components

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


Mass: 22820.111 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae (bacteria) / Gene: clpP, ADT25_23080, ADT27_15185, EYR26_04825 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M1K022, endopeptidase Clp
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 955 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate trihydrate, 3.0 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: 0.9735 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.791→30 Å / Num. obs: 154153 / % possible obs: 99.4 % / Redundancy: 16.9 % / Biso Wilson estimate: 15.01 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.021 / Rrim(I) all: 0.094 / Χ2: 1.03 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.869.50.531148000.2570.1740.5620.68796.9
1.86-1.9411.40.506151560.4390.1520.530.77198.8
1.94-2.0312.70.456152040.6770.1290.4750.86999.3
2.03-2.13140.375153480.8820.10.3891.04499.6
2.13-2.2716.50.307153290.950.0750.3171.14799.8
2.27-2.4417.30.241154160.9780.0580.2481.2499.9
2.44-2.6918.60.178154750.9890.0410.1831.287100
2.69-3.0821.20.122155520.9950.0270.1251.23100
3.08-3.8822.70.078156490.9980.0160.081.052100
3.88-30240.052162240.9990.0110.0530.73199.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3STA

3sta


Resolution: 1.8→29.639 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 7270 5.03 %
Rwork0.1865 137364 -
obs0.1883 144634 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.62 Å2 / Biso mean: 21.3653 Å2 / Biso min: 7.06 Å2
Refinement stepCycle: final / Resolution: 1.8→29.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9801 0 8 955 10764
Biso mean--24.8 28.43 -
Num. residues----1287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089946
X-RAY DIFFRACTIONf_angle_d0.88113481
X-RAY DIFFRACTIONf_chiral_restr0.0571593
X-RAY DIFFRACTIONf_plane_restr0.0051751
X-RAY DIFFRACTIONf_dihedral_angle_d8.9196380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.81150.3103960.2759145831
1.8115-1.83290.30691160.2836251151
1.8329-1.85520.28241610.2736320465
1.8552-1.87870.29241740.2649371876
1.8787-1.90340.31372140.2603409884
1.9034-1.92950.27382330.2611433689
1.9295-1.9570.29392660.2467453293
1.957-1.98620.26662390.2306468596
1.9862-2.01730.26672710.23473497
2.0173-2.05030.26952600.2135479698
2.0503-2.08570.24252540.1946486499
2.0857-2.12360.2442450.1939486199
2.1236-2.16440.19582340.18794915100
2.1644-2.20860.23132560.18584944100
2.2086-2.25660.22992830.18414822100
2.2566-2.30910.23132900.18694858100
2.3091-2.36680.242510.17644993100
2.3668-2.43080.23162760.17014847100
2.4308-2.50230.21722680.17034950100
2.5023-2.5830.23352370.1764935100
2.583-2.67520.22822600.17534947100
2.6752-2.78230.21422620.18074937100
2.7823-2.90880.23672830.17354948100
2.9088-3.0620.20282540.17184987100
3.062-3.25360.20642700.17354957100
3.2536-3.50450.20182390.17055010100
3.5045-3.85650.18462590.1645031100
3.8565-4.41290.17932370.15225090100
4.4129-5.55380.19212880.17045086100
5.5538-29.6390.20032940.19295310100
Refinement TLS params.Method: refined / Origin x: 52.435 Å / Origin y: 116.9147 Å / Origin z: 240.6991 Å
111213212223313233
T0.091 Å2-0.049 Å2-0.0074 Å2-0.0813 Å20.0007 Å2--0.1136 Å2
L0.0313 °2-0.0755 °20.034 °2-0.069 °2-0.05 °2--0.3114 °2
S0.0018 Å °-0.0017 Å °-0.0249 Å °0.0054 Å °0.0122 Å °0.0289 Å °0.0609 Å °-0.0712 Å °-0.0115 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA11 - 198
2X-RAY DIFFRACTION1allB11 - 197
3X-RAY DIFFRACTION1allC1 - 198
4X-RAY DIFFRACTION1allD10 - 197
5X-RAY DIFFRACTION1allE11 - 197
6X-RAY DIFFRACTION1allF1 - 197
7X-RAY DIFFRACTION1allG10 - 198
8X-RAY DIFFRACTION1allS1 - 1271
9X-RAY DIFFRACTION1allH1 - 8

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