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- PDB-3zrj: Complex of ClpV N-domain with VipB peptide -

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Basic information

Entry
Database: PDB / ID: 3zrj
TitleComplex of ClpV N-domain with VipB peptide
Components
  • CLPB PROTEIN
  • VIPB
KeywordsCHAPERONE/PEPTIDE / CHAPERONE-PEPTIDE COMPLEX / HSP100 PROTEINS / AAA+ PROTEINS / T6SS / SECRETION / VIRULENCE
Function / homology
Function and homology information


Type VI secretion system TssC-like / TssC1, N-terminal / TssC1, C-terminal / EvpB/VC_A0108, tail sheath N-terminal domain / EvpB/VC_A0108, tail sheath gpW/gp25-like domain / Double Clp-N motif / Clp, N-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Type VI secretion system contractile sheath large subunit
Similarity search - Component
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.94 Å
AuthorsLenherr, E.D. / Kopp, J. / Sinning, I.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Basis for the Unique Role of the Aaa+ Chaperone Clpv in Type Vi Protein Secretion.
Authors: Pietrosiuk, A. / Lenherr, E.D. / Falk, S. / Bonemann, G. / Kopp, J. / Zentgraf, H. / Sinning, I. / Mogk, A.
History
DepositionJun 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLPB PROTEIN
B: CLPB PROTEIN
X: VIPB
Y: VIPB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4265
Polymers43,3644
Non-polymers621
Water4,558253
1
A: CLPB PROTEIN
X: VIPB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7443
Polymers21,6822
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CLPB PROTEIN
Y: VIPB


Theoretical massNumber of molelcules
Total (without water)21,6822
Polymers21,6822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-35.2 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.240, 37.610, 88.130
Angle α, β, γ (deg.)90.00, 107.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CLPB PROTEIN / / CLPV


Mass: 19342.082 Da / Num. of mol.: 2 / Fragment: N-DOMAIN, RESIDUES 2-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Strain: V52 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL-1 BLUE / References: UniProt: A1EKV2
#2: Protein/peptide VIPB


Mass: 2339.798 Da / Num. of mol.: 2 / Fragment: RESIDUES 15-28 / Source method: obtained synthetically / Source: (synth.) VIBRIO CHOLERAE (bacteria) / References: UniProt: Q9KN57
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.34 Å3/Da / Density % sol: 47.36 % / Description: NONE
Crystal growTemperature: 277 K / Details: 0.1M MES PH 5.5, 17.5% (W/V) PEG 8000, 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.94→47.7 Å / Num. obs: 28218 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 1.94→2 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.332 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.94→42.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.535 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1411 5 %RANDOM
Rwork0.183 ---
obs-26807 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.689 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å2-0.62 Å2
2--2.99 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 1.94→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 4 253 3023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222849
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9823868
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.39624.848132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53515522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3721517
X-RAY DIFFRACTIONr_chiral_restr0.1380.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212096
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2261.51763
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05422846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4331086
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5184.51016
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 97 -
Rwork0.208 1856 -
obs--100 %
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)
13.48841.9751-1.20974.6172-1.30840.2259-0.26440.5225-0.1439-0.30420.31560.39230.0971-0.0194-0.05120.1623-0.0116-0.01110.13250.00030.166-7.605811.456512.9311
21.33010.43690.7348-0.01920.5491.60670.01680.21360.00930.06230.011-0.00910.00010.2965-0.02770.1008-0.0030.00520.1803-0.0080.106714.719716.105516.5602
31.0945-0.11460.67810.9521-0.40341.37970.13080.1212-0.05460.057-0.1407-0.10950.18070.34610.00990.09630.0226-0.01240.1807-0.00090.104817.9910.413622.3469
41.07010.04950.25970.3591-0.05340.81840.0279-0.05480.02320.0290.00090.04840.0034-0.0083-0.02890.1191-0.00640.0060.1026-0.00960.12333.969915.634127.0574
58.1975-4.97451.3415.1105-1.21121.8108-0.0085-0.4481-0.28330.19910.20760.04680.1286-0.1914-0.19910.1337-0.0273-0.01720.08160.05180.1589-0.92764.512730.9847
61.40090.2573-0.49710.343-0.08120.84210.10560.07130.16660.0445-0.03670.0268-0.013-0.1983-0.06890.09950.0140.01720.12930.01850.123-30.401816.927821.8327
70.8418-0.4857-0.5623-0.38070.2316.01290.14140.0354-0.07510.10460.0233-0.09990.3123-0.0083-0.16470.1405-0.0161-0.02690.16650.01730.0783-32.00869.105638.2875
82.13050.0263-0.47260.0316-0.07450.85490.04360.2160.04130.0274-0.0112-0.0940.0191-0.0924-0.03240.1046-0.00040.0240.11620.01610.1289-20.419615.040114.6361
92.83562.00280.15221.6472-2.38275.4430.17090.28290.0358-0.0518-0.07390.1639-0.06090.1611-0.0970.13630.051-0.03170.2305-0.00120.07135.774313.74242.9001
104.2772-1.17631.83993.9973-4.09588.78240.8434-0.78750.21710.5327-0.77310.1143-0.87261.128-0.07030.1954-0.29490.11970.4979-0.05470.0432-23.45118.836437.0228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 15
2X-RAY DIFFRACTION2A16 - 54
3X-RAY DIFFRACTION3A55 - 86
4X-RAY DIFFRACTION4A87 - 158
5X-RAY DIFFRACTION5B-6 - 4
6X-RAY DIFFRACTION6B5 - 76
7X-RAY DIFFRACTION7B77 - 86
8X-RAY DIFFRACTION8B87 - 158
9X-RAY DIFFRACTION9X16 - 29
10X-RAY DIFFRACTION10Y18 - 27

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