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- PDB-7m1m: Crystal structure of Pseudomonas aeruginosa ClpP1 -

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Basic information

Entry
Database: PDB / ID: 7m1m
TitleCrystal structure of Pseudomonas aeruginosa ClpP1
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Petidase
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
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsMawla, G.D. / Grant, R.A. / Baker, T.A. / Sauer, R.T.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI016892 United States
CitationJournal: Mol.Microbiol. / Year: 2021
Title: ClpP1P2 peptidase activity promotes biofilm formation in Pseudomonas aeruginosa.
Authors: Mawla, G.D. / Hall, B.M. / Carcamo-Oyarce, G. / Grant, R.A. / Zhang, J.J. / Kardon, J.R. / Ribbeck, K. / Sauer, R.T. / Baker, T.A.
History
DepositionMar 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 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
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)325,45032
Polymers323,32314
Non-polymers2,12718
Water2,828157
1
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)162,72516
Polymers161,6617
Non-polymers1,0649
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25360 Å2
ΔGint-252 kcal/mol
Surface area51220 Å2
MethodPISA
2
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)162,72516
Polymers161,6617
Non-polymers1,0649
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25460 Å2
ΔGint-256 kcal/mol
Surface area50980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.975, 97.118, 108.347
Angle α, β, γ (deg.)66.990, 85.930, 77.170
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31(chain C and (resid 4 through 8 or resid 18 through 194))
41(chain D and resid 4 through 194)
51(chain E and (resid 4 through 8 or resid 18 through 194))
61chain F
71chain G
81chain H
91chain I
101(chain J and (resid 4 through 8 or resid 18 through 194))
111(chain K and resid 4 through 194)
121chain L
131chain M
141chain N

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
11LEULEUARGARGchain AAA4 - 1944 - 194
21LEULEUARGARGchain BBB4 - 1944 - 194
31LEULEUVALVAL(chain C and (resid 4 through 8 or resid 18 through 194))CC4 - 84 - 8
32ALAALAARGARG(chain C and (resid 4 through 8 or resid 18 through 194))CC18 - 19418 - 194
41LEULEUARGARG(chain D and resid 4 through 194)DD4 - 1944 - 194
51LEULEUVALVAL(chain E and (resid 4 through 8 or resid 18 through 194))EE4 - 84 - 8
52ALAALAARGARG(chain E and (resid 4 through 8 or resid 18 through 194))EE18 - 19418 - 194
61LEULEUARGARGchain FFF4 - 1944 - 194
71LEULEUARGARGchain GGG4 - 1944 - 194
81LEULEUARGARGchain HHH4 - 1944 - 194
91LEULEUARGARGchain III4 - 1944 - 194
101LEULEUVALVAL(chain J and (resid 4 through 8 or resid 18 through 194))JJ4 - 84 - 8
102ALAALAARGARG(chain J and (resid 4 through 8 or resid 18 through 194))JJ18 - 19418 - 194
111LEULEUARGARG(chain K and resid 4 through 194)KK4 - 1944 - 194
121LEULEUARGARGchain LLL4 - 1944 - 194
131LEULEUARGARGchain MMM4 - 1944 - 194
141LEULEUARGARGchain NNN4 - 1944 - 194

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Components

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


Mass: 23094.473 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: clpP1, clpP, clpP_1, clpP_2, clpP_3, ALP65_02974, C0044_13485, CAZ10_25705, CGU42_31830, DZ962_05185, E4V10_13100, ECC04_019615, EQH76_24460, FOZ66_18665, HWN46_10325, HWN47_21130, IPC116_ ...Gene: clpP1, clpP, clpP_1, clpP_2, clpP_3, ALP65_02974, C0044_13485, CAZ10_25705, CGU42_31830, DZ962_05185, E4V10_13100, ECC04_019615, EQH76_24460, FOZ66_18665, HWN46_10325, HWN47_21130, IPC116_19025, IPC1323_26610, IPC1481_00800, IPC1505_27710, IPC1509_11515, IPC36_03810, IPC582_00530, IPC620_12795, IPC669_04255, NCTC10662_04309, NCTC12951_04915, NCTC13437_00640, PAMH19_5202, RW109_RW109_04256
Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZHR6, endopeptidase Clp
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium malonate, 53.5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→48.54 Å / Num. obs: 103306 / % possible obs: 94.2 % / Redundancy: 2.712 % / Biso Wilson estimate: 44.334 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.094 / Rrim(I) all: 0.156 / Χ2: 0.98 / Net I/σ(I): 6.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.662.6420.5571.8518571804470290.7950.69287.4
2.66-2.742.7880.5012.1121180794075970.8660.61995.7
2.74-2.822.7880.4182.5220450770573350.8960.51595.2
2.82-2.92.7670.3523.0319695743671180.9310.43295.7
2.9-32.750.3043.5419093726669420.9420.37395.5
3-3.12.7450.2694.118380701866970.9480.33195.4
3.1-3.222.7380.2314.7117494673863890.9650.28394.8
3.22-3.352.7140.1825.6916722652261610.9750.22494.5
3.35-3.52.6770.1626.4615574622158180.9780.19993.5
3.5-3.672.6120.1347.4314123593954060.9810.16691
3.67-3.872.5580.118.5712807570350070.9840.13787.8
3.87-4.112.7330.1059.6114152530651790.9860.12997.6
4.11-4.392.7150.08610.7513468508049600.990.10697.6
4.39-4.742.6980.07811.6712150464945040.9910.09696.9
4.74-5.192.7090.08811.0611444436342240.9870.10896.8
5.19-5.812.7230.1059.6910049386036900.9860.12995.6
5.81-6.712.6590.09310.338635344232470.9860.11494.3
6.71-8.212.5680.06512.866732292426220.9910.0889.7
8.21-11.612.8020.0515.416139223521910.9950.06298
11.61-48.542.7750.04416.263302123311900.9960.05496.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QWD

3qwd


Resolution: 2.6→48.54 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1998 1.94 %
Rwork0.207 101250 -
obs0.2078 103248 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.86 Å2 / Biso mean: 46.2206 Å2 / Biso min: 16.83 Å2
Refinement stepCycle: final / Resolution: 2.6→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19842 0 396 157 20395
Biso mean--56.88 34.06 -
Num. residues----2554
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12482X-RAY DIFFRACTION8.56TORSIONAL
12B12482X-RAY DIFFRACTION8.56TORSIONAL
13C12482X-RAY DIFFRACTION8.56TORSIONAL
14D12482X-RAY DIFFRACTION8.56TORSIONAL
15E12482X-RAY DIFFRACTION8.56TORSIONAL
16F12482X-RAY DIFFRACTION8.56TORSIONAL
17G12482X-RAY DIFFRACTION8.56TORSIONAL
18H12482X-RAY DIFFRACTION8.56TORSIONAL
19I12482X-RAY DIFFRACTION8.56TORSIONAL
110J12482X-RAY DIFFRACTION8.56TORSIONAL
111K12482X-RAY DIFFRACTION8.56TORSIONAL
112L12482X-RAY DIFFRACTION8.56TORSIONAL
113M12482X-RAY DIFFRACTION8.56TORSIONAL
114N12482X-RAY DIFFRACTION8.56TORSIONAL
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 (%)
2.6-2.660.35391310.3266629676087
2.66-2.730.33741450.28197353749896
2.73-2.810.31861450.25247349749495
2.81-2.910.28921440.2367276742096
2.91-3.010.29971450.2357371751696
3.01-3.130.29881450.23527327747295
3.13-3.270.25371440.21947263740795
3.27-3.440.23461430.2087232737594
3.44-3.660.26151380.20887021715992
3.66-3.940.22921370.19236901703890
3.94-4.340.20081480.17557500764898
4.34-4.970.21231470.16667429757697
4.97-6.260.25311450.21617393753896
6.26-48.540.22811410.18537206734794

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