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- PDB-6iub: Structure of Helicobacter pylori Soj protein -

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Basic information

Entry
Database: PDB / ID: 6iub
TitleStructure of Helicobacter pylori Soj protein
ComponentsSpoOJ regulator (Soj)
KeywordsDNA BINDING PROTEIN / Partition protein
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
CobQ/CobB/MinD/ParA nucleotide binding domain / : / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / SpoOJ regulator (Soj)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsChu, C.H. / Yen, C.Y. / Sun, Y.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation.
Authors: Chu, C.H. / Yen, C.Y. / Chen, B.W. / Lin, M.G. / Wang, L.H. / Tang, K.Z. / Hsiao, C.D. / Sun, Y.J.
History
DepositionNov 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SpoOJ regulator (Soj)
B: SpoOJ regulator (Soj)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2806
Polymers61,2172
Non-polymers1,0634
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-43 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.142, 93.322, 110.892
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SpoOJ regulator (Soj)


Mass: 30608.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_1139 / Production host: Escherichia coli (E. coli) / References: UniProt: O25759
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Bicine (pH 9.0), Tacsimate, PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jan 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 37426 / % possible obs: 93.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 19.23 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 3776 / % possible all: 96.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BEK

2bek


Resolution: 1.902→29.951 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.03
RfactorNum. reflection% reflection
Rfree0.2129 1949 5.35 %
Rwork0.1659 --
obs0.1684 36400 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.42 Å2 / Biso mean: 21.9 Å2 / Biso min: 5.79 Å2
Refinement stepCycle: final / Resolution: 1.902→29.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 64 494 4664
Biso mean--14.34 29.42 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084248
X-RAY DIFFRACTIONf_angle_d1.2695756
X-RAY DIFFRACTIONf_chiral_restr0.081670
X-RAY DIFFRACTIONf_plane_restr0.006716
X-RAY DIFFRACTIONf_dihedral_angle_d14.7591606
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9024-1.94990.25091280.18232255238384
1.9499-2.00260.25871320.18452340247288
2.0026-2.06160.2521400.17452440258092
2.0616-2.12810.23451390.17092455259492
2.1281-2.20410.21370.16712487262493
2.2041-2.29230.22781430.16512499264293
2.2923-2.39660.22561420.16522473261593
2.3966-2.52290.24611420.17182529267194
2.5229-2.68090.20491400.17412504264493
2.6809-2.88770.2371400.17652464260492
2.8877-3.1780.2181430.17882522266592
3.178-3.63720.21611430.16392526266992
3.6372-4.57990.18361400.1462480262090
4.5799-29.95490.17671400.15742477261785

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