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- PDB-4hh5: N-terminal domain (1-163) of ClpV1 ATPase from E.coli EAEC Sci1 T6SS. -

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Basic information

Entry
Database: PDB / ID: 4hh5
TitleN-terminal domain (1-163) of ClpV1 ATPase from E.coli EAEC Sci1 T6SS.
ComponentsPutative type VI secretion proteinType VI secretion system
KeywordsPROTEIN BINDING / Alpha helical protein / ATPase domain / SciI
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
AAA+ ATPase ClpV1 / Double Clp-N motif / Clp, N-terminal domain / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain ...AAA+ ATPase ClpV1 / Double Clp-N motif / Clp, N-terminal domain / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Type VI secretion protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDouzi, B. / Spinelli, S. / Legrand, P. / Lensi, V. / Brunet, Y.R. / Cascales, E. / Cambillau, C.
CitationJournal: To be Published
Title: Role and specificity of ClpV ATPases in T6SS secretion.
Authors: Douzi, B. / Spinelli, S. / Legrand, P. / Lensi, V. / Brunet, Y.R. / Cascales, E. / Cambillau, C.
History
DepositionOct 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4652
Polymers18,3851
Non-polymers801
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.860, 58.710, 65.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative type VI secretion protein / Type VI secretion system


Mass: 18384.877 Da / Num. of mol.: 1 / Fragment: fragment 1-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EAEC 042 / Gene: ClpV1, EC042_4530 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3GUW1
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.58 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.931 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2012
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 19805 / Num. obs: 10703 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 28.35 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 27.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1405 / % possible all: 92.1

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Processing

Software
NameVersionClassification
SHELXSphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→43.77 Å / Cor.coef. Fo:Fc: 0.9352 / Cor.coef. Fo:Fc free: 0.9338 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 512 4.78 %RANDOM
Rwork0.1853 ---
all0.1863 10703 --
obs0.1863 10703 95.84 %-
Displacement parametersBiso mean: 29.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.1693 Å20 Å20 Å2
2--4.6559 Å20 Å2
3----5.8251 Å2
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: LAST / Resolution: 2→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 1 107 1373
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081303HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.041778HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0449SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes036HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0188HARMONIC5
X-RAY DIFFRACTIONt_it01303HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion19.53
X-RAY DIFFRACTIONt_chiral_improper_torsion0164SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact01568SEMIHARMONIC4
LS refinement shellResolution: 2→2.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2342 125 4.32 %
Rwork0.179 2770 -
all0.1814 2895 -
obs-2770 95.84 %
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)
10.0638-0.13160.20660.05290.03810.0056-0.00060.0031-0.0013-0.0031-0.0013-0.0036-0.0017-0.00120.00190.0008-0.0033-0.0675-0.006-0.00920.0033-7.74090.26031.3962
20.00630.08790.07270.03-0.02920.0780.0005-0.0007-0.00150.00050.00030.00520.0032-0.0048-0.00080.0217-0.0258-0.037-0.0009-0.0044-0.0247-9.159412.853411.347
30-0.0714-0.06070.0464-0.09930.02080-0.00060.0014-0.0016-0.0019-0.00140.001-0.00120.00190.02110.02360.0154-0.00980.0077-0.00750.011619.45786.9553
40.0223-0.3082-0.28560.11120.04720.0428-0.0021-0.00170.00010.00340.0009-0.00080.00160.0040.00120.01020.01410.0455-0.00750.0238-0.00327.936816.66983.4611
50.03730.0978-0.20990.1376-0.12340.00270.0004-0.0014-0.004-0.0023-0.0026-0.0054-0.00080.00720.0023-0.0088-0.01150.05010.00190.0420.00622.71418.992313.9979
60.0521-0.0435-0.00280.0027-0.04470.00030-0.00020.0007-0.0017-0.0005-0.001-0.00020.00230.0004-0.00720.01230.02050.00290.00380.0054-2.344420.531325.5366
70.0651-0.14040.27470-0.16010.11920.0029-0.00190.0021-0.0037-0.0089-0.0043-0.0002-0.00640.006-0.0105-0.0175-0.0151-0.00170.04950.01156.141721.205727.199
80-0.0228-0.07890.0485-0.06630.027-0.0010.00230.0023-0.00020.00150.001-0.0012-0.0006-0.0005-0.0035-0.0060.03340.0060.0305-0.003814.142619.949812.7481
90-0.023-0.11610.07040.10160.0137-0.00070.00130.00140.0018-0.00180.00300.00060.00250.00780.00130.0201-0.0019-0.00140.00148.416513.6868-1.4414
100.0017-0.1-0.11180.0221-0.0820.00060.00020.00280.0022-0.0037-0.0002-0.0042-0.00110.000200.01420.05380.0136-0.01570.015-0.00191.744.656111.1149
110.001-0.0074-0.00990-0.01460.03090.0004-0.0004-0.00110.0023-0.00140.00340.0011-0.00130.0010.00390.0047-0.0212-0.0038-0.02430.0011-8.89122.52819.6108
120.0345-0.0937-0.13730.00150.18720.13360.0008-0.00180.0029-0.00530.00220.0053-0.0020.0021-0.0030.00050.00640.02360.0058-0.0243-0.007-6.77819.674819.406
130.0444-0.087-0.01620.0693-0.00650.04770.0003-0.00210.00060.00040.0003-0.004500.0001-0.0006-0.00240.0120.01640.00060.00090.00267.37695.164619.6964
140.0844-0.08680.04550.0496-0.02380.03990.0011-0.00210.0001-0.00110.0003-0.00480.0037-0.0008-0.0013-0.00510.0068-0.00660.00480.01250.00159.742712.900925.1391
150.0284-0.008-0.12640.0166-0.05390.00260.00090-0.00190.00280.00280.00240.00460.0018-0.0038-0.0114-0.019-0.007-0.00150.01070.0069-4.63187.999831.253
160.0406-0.0486-0.111700.012800.0007-0.00090.0032-0.0005-0.0003-0.00070.0014-0.0047-0.0003-0.00850.00840.01460.00420.00570.0053-13.027418.207625.7662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|10 }A1 - 10
2X-RAY DIFFRACTION2{ A|11 - A|20 }A11 - 20
3X-RAY DIFFRACTION3{ A|21 - A|30 }A21 - 30
4X-RAY DIFFRACTION4{ A|31 - A|40 }A31 - 40
5X-RAY DIFFRACTION5{ A|41 - A|50 }A41 - 50
6X-RAY DIFFRACTION6{ A|51 - A|60 }A51 - 60
7X-RAY DIFFRACTION7{ A|61 - A|70 }A61 - 70
8X-RAY DIFFRACTION8{ A|71 - A|80 }A71 - 80
9X-RAY DIFFRACTION9{ A|81 - A|90 }A81 - 90
10X-RAY DIFFRACTION10{ A|91 - A|100 }A91 - 100
11X-RAY DIFFRACTION11{ A|101 - A|110 }A101 - 110
12X-RAY DIFFRACTION12{ A|111 - A|120 }A111 - 120
13X-RAY DIFFRACTION13{ A|121 - A|130 }A121 - 130
14X-RAY DIFFRACTION14{ A|131 - A|140 }A131 - 140
15X-RAY DIFFRACTION15{ A|141 - A|150 }A141 - 150
16X-RAY DIFFRACTION16{ A|151 - A|163 }A151 - 163

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