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- PDB-7dfu: Crystal structure of Xanthomonas oryzae ClpP S68Y in complex with... -

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Basic information

Entry
Database: PDB / ID: 7dfu
TitleCrystal structure of Xanthomonas oryzae ClpP S68Y in complex with ADEP4.
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Caseinolytic protease P / Clp protease
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / serine-type endopeptidase activity / proteolysis / 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
Chem-EZA / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesXanthomonas oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 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 / 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

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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)165,94222
Polymers160,2737
Non-polymers5,66915
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22740 Å2
ΔGint-182 kcal/mol
Surface area49020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.498, 132.498, 187.833
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-575-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 25 through 91 or (resid 92...
21(chain B and (resid 25 through 124 or resid 126...
31(chain C and (resid 25 through 91 or (resid 92...
41(chain D and (resid 25 through 91 or (resid 92...
51(chain E and (resid 25 through 91 or (resid 92...
61(chain F and (resid 25 through 91 or (resid 92...
71(chain G and (resid 25 through 91 or (resid 92...

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
11TYRTYRILEILE(chain A and (resid 25 through 91 or (resid 92...AA25 - 9125 - 91
12LYSLYSLYSLYS(chain A and (resid 25 through 91 or (resid 92...AA9292
13VALVALPROPRO(chain A and (resid 25 through 91 or (resid 92...AA11 - 20111 - 201
14VALVALPROPRO(chain A and (resid 25 through 91 or (resid 92...AA11 - 20111 - 201
15VALVALPROPRO(chain A and (resid 25 through 91 or (resid 92...AA11 - 20111 - 201
16VALVALPROPRO(chain A and (resid 25 through 91 or (resid 92...AA11 - 20111 - 201
21TYRTYRASNASN(chain B and (resid 25 through 124 or resid 126...BB25 - 12425 - 124
22ARGARGLEULEU(chain B and (resid 25 through 124 or resid 126...BB126 - 169126 - 169
23GLUGLUGLUGLU(chain B and (resid 25 through 124 or resid 126...BB170170
24LEULEUARGARG(chain B and (resid 25 through 124 or resid 126...BB10 - 19910 - 199
25LEULEUARGARG(chain B and (resid 25 through 124 or resid 126...BB10 - 19910 - 199
26LEULEUARGARG(chain B and (resid 25 through 124 or resid 126...BB10 - 19910 - 199
27LEULEUARGARG(chain B and (resid 25 through 124 or resid 126...BB10 - 19910 - 199
31TYRTYRILEILE(chain C and (resid 25 through 91 or (resid 92...CC25 - 9125 - 91
32LYSLYSLYSLYS(chain C and (resid 25 through 91 or (resid 92...CC9292
33LEULEUARGARG(chain C and (resid 25 through 91 or (resid 92...CC10 - 19910 - 199
34LEULEUARGARG(chain C and (resid 25 through 91 or (resid 92...CC10 - 19910 - 199
35LEULEUARGARG(chain C and (resid 25 through 91 or (resid 92...CC10 - 19910 - 199
36LEULEUARGARG(chain C and (resid 25 through 91 or (resid 92...CC10 - 19910 - 199
41TYRTYRILEILE(chain D and (resid 25 through 91 or (resid 92...DD25 - 9125 - 91
42LYSLYSLYSLYS(chain D and (resid 25 through 91 or (resid 92...DD9292
43LEULEUGLUGLU(chain D and (resid 25 through 91 or (resid 92...DD10 - 19810 - 198
44LEULEUGLUGLU(chain D and (resid 25 through 91 or (resid 92...DD10 - 19810 - 198
45LEULEUGLUGLU(chain D and (resid 25 through 91 or (resid 92...DD10 - 19810 - 198
46LEULEUGLUGLU(chain D and (resid 25 through 91 or (resid 92...DD10 - 19810 - 198
51TYRTYRILEILE(chain E and (resid 25 through 91 or (resid 92...EE25 - 9125 - 91
52LYSLYSLYSLYS(chain E and (resid 25 through 91 or (resid 92...EE9292
53THRTHRGLUGLU(chain E and (resid 25 through 91 or (resid 92...EE18 - 19818 - 198
54THRTHRGLUGLU(chain E and (resid 25 through 91 or (resid 92...EE18 - 19818 - 198
55THRTHRGLUGLU(chain E and (resid 25 through 91 or (resid 92...EE18 - 19818 - 198
56THRTHRGLUGLU(chain E and (resid 25 through 91 or (resid 92...EE18 - 19818 - 198
61TYRTYRILEILE(chain F and (resid 25 through 91 or (resid 92...FF25 - 9125 - 91
62LYSLYSLYSLYS(chain F and (resid 25 through 91 or (resid 92...FF9292
63VALVALGLUGLU(chain F and (resid 25 through 91 or (resid 92...FF11 - 19811 - 198
64VALVALGLUGLU(chain F and (resid 25 through 91 or (resid 92...FF11 - 19811 - 198
65VALVALGLUGLU(chain F and (resid 25 through 91 or (resid 92...FF11 - 19811 - 198
66VALVALGLUGLU(chain F and (resid 25 through 91 or (resid 92...FF11 - 19811 - 198
71TYRTYRILEILE(chain G and (resid 25 through 91 or (resid 92...GG25 - 9125 - 91
72LYSLYSLYSLYS(chain G and (resid 25 through 91 or (resid 92...GG9292
73LEULEUGLUGLU(chain G and (resid 25 through 91 or (resid 92...GG10 - 19810 - 198
74LEULEUGLUGLU(chain G and (resid 25 through 91 or (resid 92...GG10 - 19810 - 198
75LEULEUGLUGLU(chain G and (resid 25 through 91 or (resid 92...GG10 - 19810 - 198
76LEULEUGLUGLU(chain G and (resid 25 through 91 or (resid 92...GG10 - 19810 - 198

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Components

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


Mass: 22896.209 Da / Num. of mol.: 7 / Mutation: S68Y
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-EZA / N-[(6aS,12S,15aS,17R,21R,23aS)-17,21-dimethyl-6,11,15,20,23-pentaoxooctadecahydro-2H,6H,11H,15H-pyrido[2,1-i]dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13]oxatetraazacyclohexadecin-12-yl]-3,5-difluoro-Nalpha-[(2E)-hept-2-enoyl]-L-phenylalaninamide


Mass: 770.862 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C39H52F2N6O8
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.17 %
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 PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9735 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 130286 / % possible obs: 99.3 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.032 / Rrim(I) all: 0.14 / Χ2: 1.113 / Net I/σ(I): 5.2 / Num. measured all: 2033446
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.974.30.494121050.2240.2430.5560.79293.6
1.97-2.056.70.495128580.1920.1960.5350.83899.3
2.05-2.1410.90.487129880.5430.1490.510.91899.9
2.14-2.2514.50.46130100.7710.1210.4760.96100
2.25-2.39160.409130010.8980.1020.4221.032100
2.39-2.5816.50.345130660.9510.0840.3551.111100
2.58-2.8419.50.265130730.9830.0590.2721.237100
2.84-3.25200.171131700.9940.0380.1751.309100
3.25-4.0923.30.092132570.9990.0190.0941.288100
4.09-3022.90.057137580.9990.0120.0591.01399.9

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIXV1.0refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3STA

3sta


Resolution: 1.901→29.692 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 5807 4.91 %
Rwork0.2174 --
obs0.2187 118374 90.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.45 Å2 / Biso mean: 20.6876 Å2 / Biso min: 1.46 Å2
Refinement stepCycle: final / Resolution: 1.901→29.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9897 0 393 517 10807
Biso mean--36.22 18.39 -
Num. residues----1296
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5744X-RAY DIFFRACTION9.387TORSIONAL
12B5744X-RAY DIFFRACTION9.387TORSIONAL
13C5744X-RAY DIFFRACTION9.387TORSIONAL
14D5744X-RAY DIFFRACTION9.387TORSIONAL
15E5744X-RAY DIFFRACTION9.387TORSIONAL
16F5744X-RAY DIFFRACTION9.387TORSIONAL
17G5744X-RAY DIFFRACTION9.387TORSIONAL
Refinement TLS params.Method: refined / Origin x: 52.1949 Å / Origin y: 116.2953 Å / Origin z: 241.2532 Å
111213212223313233
T-0.0726 Å2-0.1678 Å20.0078 Å2--0.3898 Å20.001 Å2---0.0427 Å2
L-0.0937 °2-0.0424 °20.0284 °2--0.0368 °2-0.0562 °2--0.0416 °2
S-0.0125 Å °0.0517 Å °-0.1682 Å °0.0459 Å °0.122 Å °0.0872 Å °0.1252 Å °-0.2072 Å °0.1806 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA11 - 201
2X-RAY DIFFRACTION1allB10 - 199
3X-RAY DIFFRACTION1allC10 - 199
4X-RAY DIFFRACTION1allD10 - 198
5X-RAY DIFFRACTION1allE18 - 198
6X-RAY DIFFRACTION1allF11 - 198
7X-RAY DIFFRACTION1allG10 - 198
8X-RAY DIFFRACTION1allH401
9X-RAY DIFFRACTION1allI401
10X-RAY DIFFRACTION1allJ401
11X-RAY DIFFRACTION1allK401
12X-RAY DIFFRACTION1allL401
13X-RAY DIFFRACTION1allM401
14X-RAY DIFFRACTION1allN401
15X-RAY DIFFRACTION1allO1
16X-RAY DIFFRACTION1allP1 - 7
17X-RAY DIFFRACTION1allQ3 - 568

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