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- PDB-6iuc: Structure of Helicobacter pylori Soj-ATP complex bound to DNA -

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Basic information

Entry
Database: PDB / ID: 6iuc
TitleStructure of Helicobacter pylori Soj-ATP complex bound to DNA
Components
  • DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
  • SpoOJ regulator (Soj)
KeywordsDNA BINDING PROTEIN/DNA / Partition protein / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


CobQ/CobB/MinD/ParA nucleotide binding domain / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / SpoOJ regulator (Soj)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)
C: SpoOJ regulator (Soj)
D: SpoOJ regulator (Soj)
E: DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')
F: DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,30114
Polymers137,1756
Non-polymers2,1268
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.418, 74.628, 80.351
Angle α, β, γ (deg.)71.380, 71.560, 67.830
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 264 / Label seq-ID: 13 - 276

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
SpoOJ regulator (Soj)


Mass: 30608.516 Da / Num. of mol.: 4
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: DNA chain DNA (5'-D(P*TP*CP*CP*CP*TP*GP*TP*TP*TP*CP*AP*CP*GP*TP*GP*GP*AP*AP*CP*AP*CP*CP*CP*T)-3')


Mass: 7256.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*GP*GP*GP*TP*GP*TP*TP*CP*CP*AP*CP*GP*TP*GP*AP*AP*AP*CP*AP*GP*GP*GP*A)-3')


Mass: 7483.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: MES (pH 5.6), KCl, MgCl2, PEG 8000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 18173 / % possible obs: 88 % / Redundancy: 2 % / Biso Wilson estimate: 81.7 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 8.5
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 2 % / Rmerge(I) obs: 0.419 / Num. unique obs: 2049 / CC1/2: 0.717 / % possible all: 98.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IUB

6iub


Resolution: 3.4→26.786 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.66
RfactorNum. reflection% reflection
Rfree0.2634 884 4.97 %
Rwork0.202 --
obs0.205 17786 87.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 237.46 Å2 / Biso mean: 88.9254 Å2 / Biso min: 69.76 Å2
Refinement stepCycle: final / Resolution: 3.4→26.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8212 984 128 0 9324
Biso mean--74.47 --
Num. residues----1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0169598
X-RAY DIFFRACTIONf_angle_d1.64113208
X-RAY DIFFRACTIONf_chiral_restr0.0811532
X-RAY DIFFRACTIONf_plane_restr0.011480
X-RAY DIFFRACTIONf_dihedral_angle_d13.2745602
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5153X-RAY DIFFRACTION5.583TORSIONAL
12B5153X-RAY DIFFRACTION5.583TORSIONAL
13C5153X-RAY DIFFRACTION5.583TORSIONAL
14D5153X-RAY DIFFRACTION5.583TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.61260.33691630.26023134329798
3.6126-3.89070.26611630.23323132329598
3.8907-4.28080.22981620.2063063322595
4.2808-4.8970.24621390.18912766290586
4.897-6.15730.33371450.21682718286384
6.1573-26.78690.21881120.15212089220165
Refinement TLS params.Method: refined / Origin x: 18.0889 Å / Origin y: -43.7524 Å / Origin z: -70.832 Å
111213212223313233
T0.8394 Å20.0472 Å2-0.0337 Å2-0.7537 Å2-0.0344 Å2--0.8657 Å2
L0.755 °20.2437 °2-0.378 °2-0.4085 °2-0.2372 °2--0.7194 °2
S-0.0027 Å °-0.015 Å °-0.0144 Å °-0.0148 Å °-0.0169 Å °-0.0021 Å °0.0035 Å °0.0267 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 264
2X-RAY DIFFRACTION1allA500 - 501
3X-RAY DIFFRACTION1allB1 - 264
4X-RAY DIFFRACTION1allB500 - 501
5X-RAY DIFFRACTION1allC1 - 264
6X-RAY DIFFRACTION1allC500 - 501
7X-RAY DIFFRACTION1allD1 - 264
8X-RAY DIFFRACTION1allD500 - 501
9X-RAY DIFFRACTION1allE1 - 24
10X-RAY DIFFRACTION1allF1 - 24

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