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- PDB-6iud: Structure of Helicobacter pylori Soj-ADP complex bound to DNA -

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Basic information

Entry
Database: PDB / ID: 6iud
TitleStructure of Helicobacter pylori Soj-ADP 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'-DIPHOSPHATE / DNA / DNA (> 10) / SpoOJ regulator (Soj)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 Å
AuthorsYen, C.Y. / Chu, C.H. / 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

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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)138,98114
Polymers137,1756
Non-polymers1,8068
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.773, 74.690, 80.749
Angle α, β, γ (deg.)71.540, 71.590, 67.730
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: MG / End label comp-ID: MG / Auth seq-ID: 1 - 501 / Label seq-ID: 13

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

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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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 298 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: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 49136 / % possible obs: 96 % / Redundancy: 2 % / Biso Wilson estimate: 49.72 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5041 / CC1/2: 0.72 / % possible all: 97.9

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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: 2.506→29.955 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 28.08
RfactorNum. reflection% reflection
Rfree0.2576 2441 4.97 %
Rwork0.2047 --
obs0.2073 49125 95.67 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 207.83 Å2 / Biso mean: 62.1351 Å2 / Biso min: 22.07 Å2
Refinement stepCycle: final / Resolution: 2.506→29.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8212 984 112 0 9308
Biso mean--41.2 --
Num. residues----1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0179582
X-RAY DIFFRACTIONf_angle_d1.96313180
X-RAY DIFFRACTIONf_chiral_restr0.0921532
X-RAY DIFFRACTIONf_plane_restr0.0131480
X-RAY DIFFRACTIONf_dihedral_angle_d18.3175642
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5023X-RAY DIFFRACTION11.973TORSIONAL
12B5023X-RAY DIFFRACTION11.973TORSIONAL
13C5023X-RAY DIFFRACTION11.973TORSIONAL
14D5023X-RAY DIFFRACTION11.973TORSIONAL
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 (%)
2.506-2.55710.35491390.26712626276592
2.5571-2.61270.38191480.26822847299598
2.6127-2.67340.30911520.26472829298198
2.6734-2.74030.33911440.25742772291698
2.7403-2.81430.29411510.24292811296298
2.8143-2.8970.33191520.25172810296298
2.897-2.99050.31661430.24142835297898
2.9905-3.09720.25771520.23142817296998
3.0972-3.22110.26891440.23242792293698
3.2211-3.36750.27711490.22542799294897
3.3675-3.54480.28681400.21672764290496
3.5448-3.76650.24321410.20122733287495
3.7665-4.05670.26991400.19432669280994
4.0567-4.46370.22781350.17832593272890
4.4637-5.10690.21351320.1732573270590
5.1069-6.42370.24721400.19572730287094
6.4237-29.95740.18961390.16362684282393
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)
10.85880.60990.1370.68450.18410.5035-0.04590.1531-0.04740.036-0.12390.42830.2556-0.37470.00140.51790.0184-0.06080.4987-0.12850.5582-46.062765.9342-41.6035
20.5038-0.41010.34970.2001-0.06860.60920.0722-0.3981-0.3440.3154-0.21590.42170.3241-0.38860.0020.5846-0.07040.07960.5178-0.07650.6567-48.045662.276-29.6451
30.2852-0.2498-0.05450.23720.01720.0528-0.0846-0.6302-0.51730.67920.15630.50570.62460.54850.01690.7830.0798-0.01390.60330.02620.4673-36.185266.7029-18.7806
4-0.0354-0.00440.06370.15510.12230.24920.1224-0.2266-0.35190.0174-0.23150.06040.24860.1773-0.00590.51360.0175-0.00630.4280.02030.4842-31.295166.2075-28.9177
50.0346-0.01470.11590.1385-0.02670.0544-0.0146-0.0023-0.75470.40790.2284-0.59620.82420.71420.00030.57410.0221-0.09280.44660.05090.5031-22.830171.4504-22.3898
60.23490.28390.00260.34070.10570.20850.09020.257-0.4327-0.3818-0.00970.05080.27150.4639-0.00130.45020.09620.03110.48370.02840.4838-26.726172.277-38.9479
70.2510.1655-0.07470.44540.12930.19440.07260.9678-0.4077-0.4850.1431-0.4926-0.47580.33740.00630.5380.0514-0.04360.5262-0.0070.4747-29.011668.7951-45.4185
80.81070.18-0.03880.5186-0.15210.78330.0712-0.335-0.21110.482-0.34210.18790.21-0.10190.00120.563-0.03830.10610.598-0.04440.4995-44.43986.6432-12.2919
90.5394-0.5823-0.03090.9765-0.29180.6564-0.0525-0.2715-0.14630.28030.05740.36160.0841-0.4485-0.00090.49780.00660.14020.6063-0.03090.6034-51.899485.0777-17.0007
101.0257-0.4683-0.55891.2566-0.29461.32990.05240.02120.2330.0622-0.10970.1939-0.2872-0.0721-00.33290.0316-0.02150.4324-0.06340.4364-41.896595.1476-29.2011
110.15810.0853-0.05680.08370.02860.50470.21920.12530.0760.41710.08940.04320.04630.7494-0.00440.45570.0666-0.04460.5857-0.0550.473313.010598.3364-61.7381
120.6652-0.0165-0.04950.12840.19540.5411-0.0171-0.20440.36220.3713-0.1856-0.1292-0.39180.191-0.0030.5217-0.021-0.15970.4722-0.01910.624213.7036107.9845-52.2716
130.3997-0.20930.27130.80910.41210.3353-0.1830.13830.4756-0.03620.0525-0.6082-0.37260.6097-0.00090.502-0.0382-0.08770.65660.10690.702518.8582108.2773-60.9484
140.0463-0.07120.06090.22140.09050.09570.00190.54630.4666-0.2124-0.1123-0.08430.03740.01360.00040.4740.01520.04430.56960.04850.455211.336699.6921-66.4336
150.0508-0.137-0.01230.37240.03840.01120.00240.5440.4161-0.71260.0071-0.85350.55350.4860.0010.61260.04840.08060.70580.05380.51699.103397.0903-76.032
160.2119-0.32270.18420.207-0.06530.5191-0.11710.507-0.5286-0.19660.0038-0.25070.3330.2841-0.00080.44830.06650.03850.5017-0.08630.46834.04489.6241-68.9018
170.32140.10850.22310.2115-0.14460.2957-0.1653-0.2985-0.31420.30230.2992-0.01690.41530.3189-0.00080.57870.05220.02270.3901-0.03340.44980.393290.413-55.7939
180.22820.16240.08950.2041-0.05480.16330.1398-0.6676-0.40880.8490.1223-0.18870.0641-0.27730.0050.64580.09620.05980.51790.04470.47534.505991.1801-49.2057
190.63930.3740.07091.20250.13310.6878-0.190.7940.0646-0.35310.0254-0.1855-0.04460.4107-0.00040.6121-0.0393-0.01860.62190.0980.4794-6.1943112.2324-82.479
200.3935-0.4148-0.23040.2664-0.25860.46040.11610.6670.1196-0.41140.0345-0.294-0.44960.45460.00240.6352-0.02440.03540.63060.18330.6457-0.6664119.0217-81.4137
210.9006-0.1799-0.51871.0645-0.08941.737-0.07170.0360.26810.0032-0.00630.0877-0.237-0.17270.00030.4814-0.0166-0.0560.330.02170.4856-13.3489113.8101-65.9429
220.00290.00410.00560.00550.01180.0120.0386-0.49560.13140.0170.14930.0985-0.12160.0227-0.00022.1527-0.156-0.22952.6321-0.03261.0659-12.169399.9488-17.5002
230.6981-0.0075-0.64510.4483-0.34040.57760.1427-0.0408-0.1772-0.08810.232-0.1793-0.23390.5570.00080.5934-0.10730.02120.59380.01160.4591-18.67389.841-49.9155
240.01760.0211-0.00510.0185-0.00180.0092-0.23040.1095-0.57710.1460.0397-0.10840.0352-0.1978-0.00051.9252-0.6389-0.80911.53960.0331.8433-33.869279.6036-75.4465
251.79810.17-1.48351.7182-0.30280.98710.1460.3836-0.3198-0.66810.17770.09240.4973-0.9810.00630.7239-0.0813-0.0530.7495-0.00970.5109-21.894489.0655-53.0584
26-0.0010.0024-0.0014-0.00120.0076-0.00030.23480.0691-0.35370.0018-0.0786-0.3155-0.25520.0556-0.00091.3452-0.3439-0.19632.3232-0.69811.4205-3.818499.1928-19.1776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 89 )A1 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 156 )A90 - 156
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 175 )A157 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 195 )A176 - 195
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 212 )A196 - 212
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 237 )A213 - 237
7X-RAY DIFFRACTION7chain 'A' and (resid 238 through 264 )A238 - 264
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 77 )B1 - 77
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 158 )B78 - 158
10X-RAY DIFFRACTION10chain 'B' and (resid 159 through 264 )B159 - 264
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 16 )C1 - 16
12X-RAY DIFFRACTION12chain 'C' and (resid 17 through 77 )C17 - 77
13X-RAY DIFFRACTION13chain 'C' and (resid 78 through 136 )C78 - 136
14X-RAY DIFFRACTION14chain 'C' and (resid 137 through 156 )C137 - 156
15X-RAY DIFFRACTION15chain 'C' and (resid 157 through 175 )C157 - 175
16X-RAY DIFFRACTION16chain 'C' and (resid 176 through 212 )C176 - 212
17X-RAY DIFFRACTION17chain 'C' and (resid 213 through 237 )C213 - 237
18X-RAY DIFFRACTION18chain 'C' and (resid 238 through 264 )C238 - 264
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 77 )D1 - 77
20X-RAY DIFFRACTION20chain 'D' and (resid 78 through 136 )D78 - 136
21X-RAY DIFFRACTION21chain 'D' and (resid 137 through 264 )D137 - 264
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 5 )E1 - 5
23X-RAY DIFFRACTION23chain 'E' and (resid 6 through 20 )E6 - 20
24X-RAY DIFFRACTION24chain 'E' and (resid 21 through 24 )E21 - 24
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 20 )F1 - 20
26X-RAY DIFFRACTION26chain 'F' and (resid 21 through 24 )F21 - 24

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