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- PDB-4hh6: Peptide from EAEC T6SS Sci1 SciI protein -

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Basic information

Entry
Database: PDB / ID: 4hh6
TitlePeptide from EAEC T6SS Sci1 SciI protein
Components
  • Peptide from EAEC T6SS Sci1 SciI protein
  • Putative type VI secretion protein
KeywordsPROTEIN BINDING / Alpha helical protein / ATPase domain + SciI peptide / 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
Type VI secretion protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.1Dec 3, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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: Putative type VI secretion protein
Z: Peptide from EAEC T6SS Sci1 SciI protein


Theoretical massNumber of molelcules
Total (without water)20,5872
Polymers20,5872
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-9 kcal/mol
Surface area8390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.920, 46.850, 75.530
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


Mass: 18384.877 Da / Num. of mol.: 1 / Fragment: unp residues 1-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EAEC 042 / Gene: ClpV1 from Sci1 T6SS, EC042_4530 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3GUW1
#2: Protein/peptide Peptide from EAEC T6SS Sci1 SciI protein


Mass: 2202.614 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.76 Å3/Da / Density % sol: 30.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20mM Tris, 100mM NaCl, 5%Glyc rol 10mM sodium borate pH 8.5, 1M citrate, protein+peptide 2mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Mar 16, 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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 5360 / Num. obs: 5360 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 57.65 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 5 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.2 / Num. unique all: 388 / % possible all: 98.5

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4HH5

4hh5


Resolution: 2.5→35.98 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.8909 / SU R Cruickshank DPI: 2.77 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 516 9.63 %RANDOM
Rwork0.2419 ---
all0.2439 5359 --
obs0.2439 5359 99.7 %-
Displacement parametersBiso mean: 54.97 Å2
Baniso -1Baniso -2Baniso -3
1--16.7897 Å20 Å20 Å2
2--12.4064 Å20 Å2
3---4.3833 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 0 26 1323
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081323HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.361804HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0442SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes030HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0193HARMONIC5
X-RAY DIFFRACTIONt_it01323HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.44
X-RAY DIFFRACTIONt_other_torsion26.06
X-RAY DIFFRACTIONt_chiral_improper_torsion0172SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact01558SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.79 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3215 133 8.92 %
Rwork0.2818 1358 -
all0.2855 1491 -
obs-1491 99.7 %
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)
10.0079-0.01930.01080.0179-0.00620.0035000.00010.00010.00010.00030-0.0005-0.00010.0010.0023-0.0002-0.0006-0.00020.00112.33714.9064-15.1718
20.001-0.0030.00140-0.00220.001600.0001-0.0001-0.00020.0001-0.00010.00010-0.00010.00080.0009-0.0008-0.0002-0.00030.00045.8276.2325-23.722
30-0.0170.00780-0.0050.001500.00010.0001-0.0003-0.00010.00110-0.00040.0001-0.0020.001500.00060.00070.00051.78015.4389-12.3999
40-0.0014-0.00600.00340-0.0001-0.00010.00030.0002-0.00010.0003-0.000500.0001-0.00090.00120.0003-0.00180.00010.00029.685913.7061-7.616
500.01190.02290-0.003900.00010.00010.000300-0.0001-0.00090.00020-0.0007-0.0051-0.0034-0.0010.0002-0.000218.01815.1234-11.3366
60-0.00590.00920.0032-0.00660-0.0002-0.00020.00020.00030.00060.0002-0.00080.0006-0.0004-0.0004-0.0003-0.0024-0.00070.00110.000513.06097.0175-4.815
70.00220.00030.0118000.00780-0.00050.00060.0001-0.00010-0.0002-0.00030.00010.00190.00120.00090-0.0004-0.00118.8915-3.06651.6568
80.0172-0.01990.0210.0068-0.00670.0160.00010-0.00060.00010.00010.00040.00020.0004-0.00020.00130.0007-0.0017-0.000300.000317.211-2.96332.9961
90.00250.01050.00550-0.002100-0.00020.0002-0.00010-0.0005-0.00010.0004-0.0001-0.0012-0.0035-0.00240.0002-0.0004-0.000724.15679.6306-5.2771
1000.0225-0.00340-0.01680.00510-0.00040.0006-0.00020.0001-0.00040.00010.0004-0.00010.0013-0.00230.0009-0.00040.0015-0.000517.71919.4432-14.8343
110.00130.00040.00220.00010.00640.005500.00040.0001-0.0003-0.00020.0001-0.000200.0002-0.0005-0.00080.00010.0013-0.0002-0.001712.89592.9194-18.7887
120.00130.00880.007300.0054000.00060.00010-0.000200.0003-0.00010.00020.0002-0.0034-0.0009-0.0006-0.0007-0.00122.4776-6.2016-16.3695
130-0.0032-0.00990.0104-0.00980.00240-0.0002-0.0002-0.0002-0.00050.00070-0.00030.00050.00020.00130.0016-0.00070.00070.00014.6475-2.624-10.4828
140.0009-0.0015-0.0050.00290.00170.002300.000100-0.0001-0.00020.00010.00030.0001-0.00010.00130.00110.0010-0.000918.5703-3.5137-13.9736
150.0025-0.00930.01320.0053-0.0087000.0002-0.00020-0.0002-0.00010.00060.00030.0002-0.00030.0025-0.00240.0010.0006-0.000120.8643-4.8495-4.8736
160.0043-0.0029-0.00010.0122-0.0107000.0003-0.00010-0.00010.00030.0004-0.000300.0012-0.00020.0016-0.00040.00150.0017.4859-13.7484-6.673
170.00290.019-0.01920.0165-0.00060.0195000.0004-0.0001-0.00020.00160.0002-0.00180.00020.00150.00020.00120.00160.00110.0011-1.1502-3.6331-0.0494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ Z|10 - Z|23 }Z10 - 23
2X-RAY DIFFRACTION2{ A|6 - A|10 }A6 - 10
3X-RAY DIFFRACTION3{ A|11 - A|20 }A11 - 20
4X-RAY DIFFRACTION4{ A|21 - A|30 }A21 - 30
5X-RAY DIFFRACTION5{ A|31 - A|40 }A31 - 40
6X-RAY DIFFRACTION6{ A|41 - A|50 }A41 - 50
7X-RAY DIFFRACTION7{ A|51 - A|60 }A51 - 60
8X-RAY DIFFRACTION8{ A|61 - A|70 }A61 - 70
9X-RAY DIFFRACTION9{ A|71 - A|80 }A71 - 80
10X-RAY DIFFRACTION10{ A|81 - A|90 }A81 - 90
11X-RAY DIFFRACTION11{ A|91 - A|100 }A91 - 100
12X-RAY DIFFRACTION12{ A|101 - A|110 }A101 - 110
13X-RAY DIFFRACTION13{ A|111 - A|120 }A111 - 120
14X-RAY DIFFRACTION14{ A|121 - A|130 }A121 - 130
15X-RAY DIFFRACTION15{ A|131 - A|140 }A131 - 140
16X-RAY DIFFRACTION16{ A|141 - A|150 }A141 - 150
17X-RAY DIFFRACTION17{ A|151 - A|162 }A151 - 162

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