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- PDB-7npe: Vibrio cholerae ParA2-ADP -

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Basic information

Entry
Database: PDB / ID: 7npe
TitleVibrio cholerae ParA2-ADP
ComponentsAAA family ATPase
KeywordsDNA BINDING PROTEIN / ATPase / Chromosome segregation / Bacterial cell division / Hydrolase
Function / homologyAAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-DIPHOSPHATE / Chromosome partitioning protein ParA
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsParker, A.V. / Bergeron, J.R.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The cryo-EM structure of the bacterial type I segregation filament reveals ParA s conformational plasticity upon DNA binding
Authors: Parker, A.V. / Mann, D. / Tzokov, S.B. / Hwang, L.C. / Bergeron, J.R.C.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _cell.angle_alpha / _cell.angle_beta ..._cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _reflns.B_iso_Wilson_estimate / _software.version / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Polymer geometry
Details: Replacement has improved geometry suggested by the reviewer
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AAA family ATPase
B: AAA family ATPase
C: AAA family ATPase
D: AAA family ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,75414
Polymers185,7644
Non-polymers1,99010
Water00
1
A: AAA family ATPase
B: AAA family ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9698
Polymers92,8822
Non-polymers1,0876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-81 kcal/mol
Surface area31610 Å2
MethodPISA
2
C: AAA family ATPase
D: AAA family ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7856
Polymers92,8822
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-77 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.205, 199.205, 260.066
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 through 7 and (name N...
21(chain C and (resid 4 through 9 or resid 11...
31(chain D and ((resid 4 through 7 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLNGLN(chain A and ((resid 4 through 7 and (name N...AA4 - 74 - 7
12LYSLYSMGMG(chain A and ((resid 4 through 7 and (name N...AA - F4 - 4514
13LYSLYSMGMG(chain A and ((resid 4 through 7 and (name N...AA - F4 - 4514
14LYSLYSMGMG(chain A and ((resid 4 through 7 and (name N...AA - F4 - 4514
15LYSLYSMGMG(chain A and ((resid 4 through 7 and (name N...AA - F4 - 4514
21LYSLYSILEILE(chain C and (resid 4 through 9 or resid 11...CC4 - 94 - 9
22ASNASNGLNGLN(chain C and (resid 4 through 9 or resid 11...CC11 - 1411 - 14
23LEULEUGLNGLN(chain C and (resid 4 through 9 or resid 11...CC15 - 1715 - 17
24METMETMGMG(chain C and (resid 4 through 9 or resid 11...CC - L3 - 4513
25METMETMGMG(chain C and (resid 4 through 9 or resid 11...CC - L3 - 4513
26METMETMGMG(chain C and (resid 4 through 9 or resid 11...CC - L3 - 4513
27METMETMGMG(chain C and (resid 4 through 9 or resid 11...CC - L3 - 4513
31LYSLYSGLNGLN(chain D and ((resid 4 through 7 and (name N...DD4 - 74 - 7
32METMETADPADP(chain D and ((resid 4 through 7 and (name N...DD - M3 - 4503
33METMETADPADP(chain D and ((resid 4 through 7 and (name N...DD - M3 - 4503
34METMETADPADP(chain D and ((resid 4 through 7 and (name N...DD - M3 - 4503
35METMETADPADP(chain D and ((resid 4 through 7 and (name N...DD - M3 - 4503

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Components

#1: Protein
AAA family ATPase / Chromosome (Plasmid) partitioning protein ParA / Chromosome partitioning protein ParA / ParA family ...Chromosome (Plasmid) partitioning protein ParA / Chromosome partitioning protein ParA / ParA family protein / Plasmid partition protein A / ParA2vc / ParA2


Mass: 46440.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: parA, BC353_10845, C9J66_03480, ERS013138_01197, ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013197_04093, ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, ...Gene: parA, BC353_10845, C9J66_03480, ERS013138_01197, ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013197_04093, ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, ERS013206_01885, F0315_18570, FLM02_03395, FXF03_20770, HPY05_13545
Production host: Escherichia coli (E. coli) / References: UniProt: A0A085S0Z4
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestY

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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: 4.01 Å3/Da / Density % sol: 69.32 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 24 %w/v PEG 1500, 20% w/v glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.18→52.59 Å / Num. obs: 49709 / % possible obs: 96.38 % / Redundancy: 2 % / Biso Wilson estimate: 128.81 Å2 / Rmerge(I) obs: 0.02072 / Net I/σ(I): 0.98
Reflection shellResolution: 3.184→3.298 Å / Rmerge(I) obs: 0.5636 / Num. unique obs: 3364 / % possible all: 66.68

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NPD

7npd


Resolution: 3.2→52.59 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 2436 4.95 %
Rwork0.238 46800 -
obs0.24 49236 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 294.56 Å2 / Biso mean: 126.2909 Å2 / Biso min: 66.13 Å2
Refinement stepCycle: final / Resolution: 3.2→52.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11921 0 124 0 12045
Biso mean--112.73 --
Num. residues----1602
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4528X-RAY DIFFRACTION17.599TORSIONAL
12C4528X-RAY DIFFRACTION17.599TORSIONAL
13D4528X-RAY DIFFRACTION17.599TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.270.3918840.36991679176360
3.27-3.340.41971270.39342566269392
3.34-3.410.42341460.34052751289799
3.41-3.50.37251360.313427842920100
3.5-3.590.35781280.304828022930100
3.59-3.70.33641410.286727892930100
3.7-3.820.35371320.272828172949100
3.82-3.960.31581490.273327962945100
3.96-4.110.30671660.266827852951100
4.11-4.30.27651580.217627982956100
4.3-4.530.25071470.208928402987100
4.53-4.810.27481460.200928222968100
4.81-5.180.22671280.223428482976100
5.18-5.70.26821690.250128543023100
5.7-6.530.30121620.261128673029100
6.53-8.220.26631500.247229343084100
8.22-52.590.24051670.19623068323599
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)
11.77810.3290.58410.55110.0621-0.03210.1562-0.49930.26480.58050.0777-0.14930.2527-0.3822-0.06111.2755-0.05690.03091.24310.15520.9237-41.514860.9317.4427
21.46870.33431.05332.229-0.30031.71210.2131-0.2055-0.31430.3553-0.11740.00170.5191-0.3405-0.10250.937-0.2160.03870.9176-0.00590.8592-42.457762.9182-11.3663
32.16321.30790.31621.64840.56391.46450.22540.40650.1196-0.0324-0.1047-0.2231-0.31650.2779-0.13580.7544-0.2087-0.01531.02690.11090.8648-13.050583.8019-23.7755
42.48410.28170.1611.95790.29084.0710.01230.4260.0013-0.0292-0.1796-0.05090.19390.24350.17750.6806-0.0373-0.12131.0023-0.0390.8634-14.688870.0569-21.7678
53.7-1.18482.97711.6384-0.05425.95120.4912-0.55250.12550.76660.67930.8339-0.4285-0.4216-0.69291.00990.03490.43550.97430.13331.2724-92.0037119.4382-10.4725
60.32140.44220.72051.9834-0.48752.7882-0.5717-1.8442-0.09390.16490.8115-0.2302-0.4324-0.6194-0.34471.2676-0.0310.06911.4965-0.18321.3508-58.0162100.390110.727
71.52290.1025-1.73791.76040.49032.40270.2832-0.54870.34820.1896-0.126-0.07520.14290.4289-0.15680.8383-0.25910.02651.2303-0.10520.9176-57.5466107.53043.2802
82.5708-0.0311.09082.5906-0.71681.76390.2574-0.96151.5384-0.35460.0015-0.3492-0.3381-0.4390.02391.26080.02910.2981.0508-0.0551.3838-70.4465120.0292-8.3724
91.5404-0.57990.10352.9281-0.77851.77750.7653-0.4021.16680.1889-0.46520.8648-1.05561.4231-0.21591.3097-0.52420.25840.8913-0.01681.5437-63.0624117.6703-15.1898
100.8377-0.0638-0.46730.92090.67242.07120.73841.74210.5229-1.2480.28530.0037-0.9473-0.6815-0.60411.3270.13430.23871.52120.26231.1502-63.5672104.7198-24.0173
114.1648-1.64340.29390.77150.53873.17420.1893-0.5274-0.07680.91370.10080.25310.15160.293-0.2061.1285-0.1998-0.11221.052-0.20150.739-57.89100.5291-18.5416
121.4096-0.45760.20611.47070.11523.1237-0.15360.06360.02790.45310.3238-0.48550.42560.5434-0.08770.8186-0.1156-0.12940.98980.01410.8924-58.175494.4141-8.3889
131.5649-0.218-0.42731.08540.74530.80310.5411.09810.24380.4093-0.15640.2324-0.0345-0.1674-0.17990.79230.0215-0.01171.4004-0.02270.9524-92.422387.8057-24.2427
142.19770.9271-0.05541.75140.10250.5188-0.2220.23190.7445-0.5411-0.08370.6383-1.09920.4220.29390.47960.0812-0.00411.6033-0.11330.7961-88.581992.2737-27.9813
153.18040.4661-0.08351.713-0.19182.53870.01440.70880.1124-0.0514-0.21550.1995-0.3174-0.18260.14750.87120.10320.12131.17430.06780.964-92.0305103.0564-20.7557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 104 )A4 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 406 )A105 - 406
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 154 )B4 - 154
4X-RAY DIFFRACTION4chain 'B' and (resid 155 through 407 )B155 - 407
5X-RAY DIFFRACTION5chain 'C' and (resid 3 through 32 )C3 - 32
6X-RAY DIFFRACTION6chain 'C' and (resid 33 through 54 )C33 - 54
7X-RAY DIFFRACTION7chain 'C' and (resid 55 through 174 )C55 - 174
8X-RAY DIFFRACTION8chain 'C' and (resid 175 through 229 )C175 - 229
9X-RAY DIFFRACTION9chain 'C' and (resid 230 through 263 )C230 - 263
10X-RAY DIFFRACTION10chain 'C' and (resid 264 through 303 )C264 - 303
11X-RAY DIFFRACTION11chain 'C' and (resid 304 through 325 )C304 - 325
12X-RAY DIFFRACTION12chain 'C' and (resid 326 through 406 )C326 - 406
13X-RAY DIFFRACTION13chain 'D' and (resid 3 through 136 )D3 - 136
14X-RAY DIFFRACTION14chain 'D' and (resid 137 through 179 )D137 - 179
15X-RAY DIFFRACTION15chain 'D' and (resid 180 through 407 )D180 - 407

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