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- PDB-3zri: N-domain of ClpV from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 3zri
TitleN-domain of ClpV from Vibrio cholerae
ComponentsCLPB PROTEIN
KeywordsCHAPERONE / HSP100 PROTEINS / AAA+ PROTEINS / T6SS / SECRETION / VIRULENCE
Function / homologyDouble Clp-N motif / Clp, N-terminal domain / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.8 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 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
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_mod / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLPB PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,4361
Polymers19,4361
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CLPB PROTEIN

A: CLPB PROTEIN


Theoretical massNumber of molelcules
Total (without water)38,8722
Polymers38,8722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2920 Å2
ΔGint-17.2 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.898, 72.990, 73.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CLPB PROTEIN / CLPV


Mass: 19435.873 Da / Num. of mol.: 1 / 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): BL21(DE3) / Variant (production host): XL-1 BLUE / References: UniProt: A1EKV2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.35 Å3/Da / Density % sol: 47.33 % / Description: NONE
Crystal growTemperature: 291 K / Details: 0.2M NAACETATE PH 7.0, 20% (W/V) PEG 3350, 18C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 5, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→36 Å / Num. obs: 18149 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.234 / % possible all: 95.4

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.8→35.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.61 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.DUE TO LESS THAN 100% INCORPORATION OF SEMET, ONLY A FRACTION WAS MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.218 908 5 %RANDOM
Rwork0.191 ---
obs0.193 17241 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: 23.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0 Å2
2---0.37 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 0 87 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211400
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.9741913
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.91324.55968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80715256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.336159
X-RAY DIFFRACTIONr_chiral_restr0.1420.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211052
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_it1.3791.5856
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24921390
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4033544
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3144.5515
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: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 66 -
Rwork0.272 1244 -
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)
12.4892-2.80731.6297.1572-7.47636.2098-0.0680.04160.08470.0786-0.1313-0.3391-0.10760.31110.19930.06980.003-0.02640.115-0.02070.098411.134-42.789-3.2709
20.61770.88541.27142.2924-1.0263-0.56860.13330.157-0.01-0.2201-0.1019-0.314-0.04710.0493-0.03140.15530.07710.20920.08970.10210.17195.3876-19.2813-19.3241
31.4060.55980.85310.27760.12931.81430.0953-0.0370.1796-0.1374-0.08830.0146-0.2748-0.0737-0.0070.12420.0452-0.00390.05030.02950.129-6.2987-11.837-13.9582
44.47420.10090.64874.24550.91370.93450.032-0.12930.3063-0.09690.1308-0.0471-0.0670.0228-0.16270.0306-0.03430.00950.0727-0.00210.12669.7533-11.7025-5.5114
50.6855-0.7596-0.07641.39350.00830.80840.0660.0091-0.0021-0.1205-0.0607-0.04530.0062-0.0611-0.00530.05810.01230.00430.07270.00550.0935-4.6024-27.2909-13.0668
61.2020.15670.8910.4095-0.0241.98890.08870.0544-0.0068-0.0609-0.07490.12890.0215-0.2033-0.01380.0450.0491-0.03040.10030.00340.0979-14.5326-22.9659-16.9367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 5
2X-RAY DIFFRACTION2A6 - 29
3X-RAY DIFFRACTION3A30 - 75
4X-RAY DIFFRACTION4A76 - 89
5X-RAY DIFFRACTION5A90 - 130
6X-RAY DIFFRACTION6A131 - 158

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