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- PDB-3pxi: Structure of MecA108:ClpC -

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Basic information

Entry
Database: PDB / ID: 3pxi
TitleStructure of MecA108:ClpC
Components
  • Adapter protein mecA 1
  • Negative regulator of genetic competence ClpC/MecB
KeywordsPROTEIN BINDING / ClpB / proteolysis / ClpC / ClpX / Hsp100/Clp / AAA+ proteins
Function / homology
Function and homology information


negative regulation of establishment of competence for transformation / negative regulation of sporulation resulting in formation of a cellular spore / establishment of competence for transformation / sporulation resulting in formation of a cellular spore / protein-macromolecule adaptor activity / ATP hydrolysis activity / ATP binding
Similarity search - Function
MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain ...MecA, C-terminal domain superfamily / Negative regulator of genetic competence, MecA / Negative regulator of genetic competence (MecA) / UVR domain / UVR domain profile. / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Negative regulator of genetic competence ClpC/MecB / Adapter protein MecA 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.926 Å
AuthorsWang, F. / Mei, Z.Q. / Wang, J.W. / Shi, Y.G.
CitationJournal: Nature / Year: 2011
Title: Structure and mechanism of the hexameric MecA-ClpC molecular machine.
Authors: Wang, F. / Mei, Z.Q. / Qi, Y. / Yan, C.G. / Hu, Q. / Wang, J.W. / Shi, Y.G.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Adapter protein mecA 1
A: Negative regulator of genetic competence ClpC/MecB
b: Adapter protein mecA 1
B: Negative regulator of genetic competence ClpC/MecB
c: Adapter protein mecA 1
C: Negative regulator of genetic competence ClpC/MecB


Theoretical massNumber of molelcules
Total (without water)293,0016
Polymers293,0016
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.806, 141.806, 656.078
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Adapter protein mecA 1


Mass: 13080.513 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 108-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mecA, BSU11520 / Plasmid: pET-27a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P37958
#2: Protein Negative regulator of genetic competence ClpC/MecB


Mass: 84586.438 Da / Num. of mol.: 3 / Mutation: E280A, E618A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: clpC, mecB, BSU00860 / Plasmid: pET-27a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P37571

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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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 10% PEG 3350, 400mM magnesium formate, 100mM MES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 6.926→49.153 Å / Num. obs: 7032 / % possible obs: 99.2 % / Redundancy: 8.7 % / Biso Wilson estimate: 486 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 26.31
Reflection shellResolution: 6.9→7.15 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PXG, 1QVR

3pxg

1qvr


Resolution: 6.926→49.153 Å / SU ML: 1.13 / σ(F): 1.34 / Phase error: 46.1 / Stereochemistry target values: ML
Details: THIS IS A 6.9A STRUCTURE, SO ONLY THE MAIN CHAIN CONFIRMATION AND DOMAIN ORIENTATION INFORMATION ARE MEANINGFUL. RESIDUE (C ALA 280) AND RESIDUE (C ILE 299) IS LINKED DUE TO THE POOR DENSITY. ...Details: THIS IS A 6.9A STRUCTURE, SO ONLY THE MAIN CHAIN CONFIRMATION AND DOMAIN ORIENTATION INFORMATION ARE MEANINGFUL. RESIDUE (C ALA 280) AND RESIDUE (C ILE 299) IS LINKED DUE TO THE POOR DENSITY. RESIDUE GLU 664 AND RESIDUE LYS 686 IN CHAIN A, B, C SHOULD BE LINKED BUT THEY ARE NOT PROPERLY LINKED DUE TO THE POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.4219 332 4.76 %thin Shell
Rwork0.4074 ---
obs0.4081 6977 99.25 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 648.396 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-77.4234 Å2-0 Å2-0 Å2
2--77.4234 Å20 Å2
3----154.8468 Å2
Refinement stepCycle: LAST / Resolution: 6.926→49.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18645 0 0 0 18645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01118824
X-RAY DIFFRACTIONf_angle_d1.49325312
X-RAY DIFFRACTIONf_dihedral_angle_d18.77180
X-RAY DIFFRACTIONf_chiral_restr0.0942976
X-RAY DIFFRACTIONf_plane_restr0.0053282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
6.9263-7.150.49231760.47053195
8.7184-49.1540.40021560.39133450
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)
10.22960.22080.18970.0381-0.01020.1313-0.1721-0.9641-0.35440.1355-0.7796-1.01170.41521.3037-1.57846.1979-0.50430.15465.48480.64146.4991-67.4403-68.27430.5902
2-0.038-0.09930.0670.2690.0235-0.0830.3684-0.4109-2.47280.58850.0626-0.32950.87181.30240.84263.7492-0.86770.71624.94480.67116.9326-35.4469-20.249113.0666
30.33520.0881-0.41510.4338-0.10290.50570.73210.2404-0.3253-0.6396-0.9949-0.5024-0.30040.2269-0.9035.3442-0.8768-1.39068.00160.1814.5736-26.37090.794765.6952
40.12630.0226-0.22660.4712-0.33850.1946-1.44430.08263.04270.0691-0.9094-0.3187-1.70750.2763-2.48539.15770.71670.79532.7717-0.34266.318-54.3672-45.82862.868
5-0.11170.0596-0.0050.65820.58960.7788-0.0132-0.16180.3069-0.6232-1.6278-0.6397-0.92050.5513-1.36124.7033-0.0242-0.20927.08590.46644.189-30.7129-8.07733.4914
62.9287-0.4819-0.58770.4055-0.13680.60650.147-0.82582.14960.48480.2939-0.25590.35040.41181.60696.7462-6.6962-2.58978.1184.24917.3151-34.1005-8.285988.1306
70.72340.35910.36770.7428-0.13520.56180.7188-0.5444-1.07870.52720.4954-0.5776-0.11641.57630.97366.4331.5719-0.32146.44220.57255.0234-70.7204-10.196437.1104
80.8727-0.36440.7171.0928-0.47252.09670.013-0.28830.7817-0.2696-1.3757-1.0168-1.01021.1861-4.69435.2844-0.70340.44255.1103-0.47494.9636-65.6754-7.731270.57
91.80251.02561.16131.73710.04351.74050.3949-1.69050.92361.2128-2.5203-1.98660.6752-1.0891-3.31834.1345-0.6763-0.30084.00570.23665.8387-81.6437-30.953587.2034
100.456-0.5241-0.0740.23210.0740.34-0.24370.98660.0465-0.36410.153.23730.1373-1.0340.16536.0789-0.3931-0.25864.39050.92714.6739-84.1452-28.02082.8352
112.8984-0.0490.37541.0659-0.57611.66010.7715-1.1081.8074-3.5583-1.2734-1.35972.40050.8145-0.60110.15640.68451.07025.13830.51966.0218-60.30817.810932.9744
120.32420.2610.66241.67560.45031.223-0.196-0.82790.9837-0.7081-0.42450.31350.3416-0.7979-1.00437.4767-0.46470.47234.16720.06624.6846-64.69586.381684.7563
130.6970.51490.04851.0994-0.57561.0198-0.2315-0.22282.0684-0.63542.6721-0.041-2.1352-0.0572.65610.3139-0.55170.84965.2908-0.18565.5443-116.654-1.077919.862
140.3730.31310.23041.1208-0.68240.4157-1.5529-0.619-0.1487-1.16070.05312.682-1.2254-0.7607-1.738910.3735-1.8893-2.084613.96894.49378.5831-101.669518.391547.5234
150.2913-0.33940.65710.9569-0.21930.1349-0.1266-1.2962.2685-1.7534-1.881.492-2.6437-0.9999-2.99097.26720.1545-1.16156.5473-0.57335.3-111.03258.761981.8664
160.277-0.04850.12360.15770.10420.1468-1.21411.3323-0.2104-0.4036-0.5559-1.79210.4466-0.7871-1.41629.5563-0.9389-2.48117.4124-0.660612.7403-134.2772-24.17053.3392
170.5726-0.03040.21030.3458-0.11690.441-0.1363-1.32041.17571.02310.59121.447-0.9521-0.32841.003610.03213.0179-0.21376.16620.820310.3648-106.967621.390515.1792
180.38350.08760.0610.75740.19190.3193-2.4255-0.0154-0.3208-0.2055-1.3355-1.9795-0.263-0.8846-0.678513.1920.81375.607318.03564.187729.0204-93.734535.573660.3817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN a
2X-RAY DIFFRACTION2CHAIN b
3X-RAY DIFFRACTION3CHAIN c
4X-RAY DIFFRACTION4CHAIN A AND RESID 3:149
5X-RAY DIFFRACTION5CHAIN B AND RESID 3:145
6X-RAY DIFFRACTION6CHAIN C AND RESID 2:146
7X-RAY DIFFRACTION7CHAIN A AND RESID 155:340
8X-RAY DIFFRACTION8CHAIN B AND RESID 156:340
9X-RAY DIFFRACTION9CHAIN C AND RESID 156:340
10X-RAY DIFFRACTION10CHAIN A AND RESID 341:484
11X-RAY DIFFRACTION11CHAIN B AND RESID 341:484
12X-RAY DIFFRACTION12CHAIN C AND RESID 341:484
13X-RAY DIFFRACTION13CHAIN A AND RESID 492:712
14X-RAY DIFFRACTION14CHAIN B AND RESID 492:712
15X-RAY DIFFRACTION15CHAIN C AND RESID 492:712
16X-RAY DIFFRACTION16CHAIN A AND RESID 715:807
17X-RAY DIFFRACTION17CHAIN B AND RESID 715:807
18X-RAY DIFFRACTION18CHAIN C AND RESID 715:807

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