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- PDB-6bek: Structure of sIHF bound to an 8bp palindromic DNA -

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Basic information

Entry
Database: PDB / ID: 6bek
TitleStructure of sIHF bound to an 8bp palindromic DNA
Components
  • DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
  • SCO1480
KeywordsDNA BINDING PROTEIN/DNA / nucleic associated proteins / Streptomyces coelicolor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nucleoid / chromosome condensation / DNA binding / cytoplasm
Similarity search - Function
: / S13-like H2TH domain / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13 family profile. / Ribosomal protein S13-like, H2TH / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / Integration host factor
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGuarne, A. / Nanji, T.N. / Shen, Y.
Citation
#1: Journal: Nucleic Acids Res. / Year: 2013
Title: A novel nucleoid-associated protein specific to the actinobacteria.
Authors: Swiercz, J.P. / Nanji, T. / Gloyd, M. / Guarne, A. / Elliot, M.A.
History
DepositionOct 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SCO1480
B: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
C: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
D: SCO1480
E: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
F: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9378
Polymers32,8596
Non-polymers782
Water6,071337
1
A: SCO1480
B: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
C: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4694
Polymers16,4303
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: SCO1480
E: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
F: DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4694
Polymers16,4303
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.260, 72.110, 103.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SCO1480


Mass: 11576.345 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO1480 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KXR9
#2: DNA chain
DNA (5'-D(*CP*AP*TP*GP*CP*AP*TP*G)-3')


Mass: 2426.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M HEPES pH 7.6, 0.2 M KSCN, 19% (w/v) PEG 3350, and 5% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2013 / Details: Double silicon (111) crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 35669 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.977 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.028 / Χ2: 1.086 / Net I/σ(I): 22.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1740 / CC1/2: 0.977 / Rpim(I) all: 0.162 / Χ2: 0.695 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ITQ

4itq


Resolution: 1.7→34.38 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.55
RfactorNum. reflection% reflection
Rfree0.2337 1665 4.76 %
Rwork0.201 --
obs0.2025 34996 98.56 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 644 2 338 2353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012133
X-RAY DIFFRACTIONf_angle_d1.1632989
X-RAY DIFFRACTIONf_dihedral_angle_d21.247877
X-RAY DIFFRACTIONf_chiral_restr0.055333
X-RAY DIFFRACTIONf_plane_restr0.006284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.2851360.22712745X-RAY DIFFRACTION99
1.75-1.80650.24241380.21922751X-RAY DIFFRACTION100
1.8065-1.87110.28291380.2242767X-RAY DIFFRACTION100
1.8711-1.9460.25321400.23372793X-RAY DIFFRACTION100
1.946-2.03450.29041380.22782766X-RAY DIFFRACTION100
2.0345-2.14180.24971410.20882812X-RAY DIFFRACTION100
2.1418-2.2760.25511380.21592769X-RAY DIFFRACTION100
2.276-2.45160.26971400.21052811X-RAY DIFFRACTION100
2.4516-2.69830.23751410.21122819X-RAY DIFFRACTION100
2.6983-3.08850.28031410.22292838X-RAY DIFFRACTION100
3.0885-3.89030.2051250.19132464X-RAY DIFFRACTION86
3.8903-34.38680.19671490.17452996X-RAY DIFFRACTION99
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)
13.47170.2955-2.38272.4904-1.8535.7269-0.367-1.11950.14350.83290.1698-0.0748-0.69380.37-0.08640.56440.2974-0.18560.6382-0.21410.304547.983425.9586161.2703
22.9694-1.7296-0.28263.59220.35253.0031-0.1909-0.26690.313-0.11060.0163-0.1152-0.20990.0560.14350.18430.0579-0.04930.214-0.02520.224549.090221.8071145.9428
32.82030.3283-2.14621.2496-0.04714.14380.219-0.15720.2778-0.0517-0.1854-0.5577-0.76550.7456-0.17530.29220.01350.06690.2601-0.03930.295755.926319.1017139.9909
41.8969-0.9319-1.38941.95861.49474.0067-0.0071-0.2931-0.09520.4780.32760.22850.2688-0.1676-0.36330.27250.0926-0.01530.31330.03450.238354.24620.9405147.0957
51.0207-0.78122.04462.4603-0.73494.40290.0571-0.1356-0.12420.12050.44490.16890.5703-0.6311-0.42550.27040.0491-0.04120.29240.0380.252250.40062.0931145.261
62.3051-2.46061.84884.1522-1.7672.2385-0.1259-0.70780.17181.05920.2535-0.0769-0.2004-0.1648-0.0060.38280.0398-0.01190.3342-0.07690.285270.051761.9155157.4752
72.7749-0.97140.1014.39380.34722.93430.21880.11390.145-0.2897-0.1901-0.07130.12650.1986-0.00560.25330.0701-0.03720.2097-0.00570.199970.393257.3807145.6625
80.66720.6795-0.32961.7921-0.40640.62990.02150.2961-0.0714-0.89170.0994-0.2866-0.4238-0.0335-0.02790.48440.0610.07450.2346-0.0010.220876.434254.7036139.7139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 13:33
2X-RAY DIFFRACTION2chain A and resid 34:87
3X-RAY DIFFRACTION3chain A and resid 88:103
4X-RAY DIFFRACTION4chain B and resid 1:8
5X-RAY DIFFRACTION5chain C and resid 1:8
6X-RAY DIFFRACTION6chain D and resid 18:33
7X-RAY DIFFRACTION7chain D and resid 34:87
8X-RAY DIFFRACTION8chain D and resid 88:102

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