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- PDB-4qpq: Mechanistic basis of plasmid-specific DNA binding of the F plasmi... -

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Basic information

Entry
Database: PDB / ID: 4qpq
TitleMechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM
Components
  • Relaxosome protein TraM
  • sbmA DNA1
  • sbmA DNA2
KeywordsTRANSCRIPTION/DNA / RHH Motif / DNA Binding / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


DNA binding / cytoplasm
Similarity search - Function
TraM protein, DNA-binding / Relaxosome protein TraM / TraM, DNA-binding domain / TraM protein, DNA-binding / Integration host factor (IHF)-like DNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Relaxosome protein TraM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.106 Å
AuthorsPeng, Y. / Lu, J. / Wong, J. / Edwards, R.A. / Frost, L.S. / Glover, J.N.M.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Mechanistic Basis of Plasmid-Specific DNA Binding of the F Plasmid Regulatory Protein, TraM.
Authors: Peng, Y. / Lu, J. / Wong, J.J. / Edwards, R.A. / Frost, L.S. / Mark Glover, J.N.
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Relaxosome protein TraM
B: Relaxosome protein TraM
C: Relaxosome protein TraM
D: Relaxosome protein TraM
E: Relaxosome protein TraM
F: Relaxosome protein TraM
G: Relaxosome protein TraM
H: Relaxosome protein TraM
P: sbmA DNA1
Q: sbmA DNA2


Theoretical massNumber of molelcules
Total (without water)65,35910
Polymers65,35910
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20580 Å2
ΔGint-162 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.057, 87.057, 217.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 2:51 )
21chain B and (resseq 2:51 )
31chain C and (resseq 2:51 )
41chain D and (resseq 2:51 )
51chain E and (resseq 2:51 )
61chain F and (resseq 2:51 )
71chain G and (resseq 2:51 )
81chain H and (resseq 2:51 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 2 - 51 / Label seq-ID: 1 - 50

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 2:51 )AA
2chain B and (resseq 2:51 )BB
3chain C and (resseq 2:51 )CC
4chain D and (resseq 2:51 )DD
5chain E and (resseq 2:51 )EE
6chain F and (resseq 2:51 )FF
7chain G and (resseq 2:51 )GG
8chain H and (resseq 2:51 )HH

NCS oper:
IDCodeMatrixVector
1given(-0.955814, -0.078361, 0.283336), (0.225301, -0.814385, 0.534806), (0.188837, 0.57501, 0.796055)-62.2052, 65.470398, -13.3782
2given(0.993804, 0.111114, -0.002758), (-0.102919, 0.92931, 0.354671), (0.041971, -0.35219, 0.934987)-40.5914, 11.7165, 10.7568
3given(-0.961199, 0.118068, 0.249314), (0.131972, -0.596828, 0.791441), (0.242241, 0.793635, 0.558089)-105.359001, 69.199303, -18.589001
4given(-0.973357, 0.224862, 0.044863), (0.211116, 0.95522, -0.207329), (-0.089475, -0.192334, -0.977242)-92.423302, 5.92663, -40.789001
5given(0.95245, 0.179377, -0.246299), (-0.12593, -0.504333, -0.854277), (-0.277454, 0.844673, -0.457763)-69.218102, 21.1262, -54.327
6given(-0.999002, -0.042894, 0.012418), (-0.041197, 0.992585, 0.114362), (-0.017231, 0.113736, -0.993362)-49.560799, 4.5565, -48.917702
7given(0.940784, -0.14108, -0.308256), (-0.316061, -0.693855, -0.647048), (-0.1226, 0.70616, -0.697358)-26.115299, 21.422899, -59.280102
DetailsFour dimers bound to double stranded DNA

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Components

#1: Protein
Relaxosome protein TraM


Mass: 6017.867 Da / Num. of mol.: 8 / Fragment: F-Tram RHH Domain, UNP residues 2-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: traM, ECOK12F071 / Production host: Escherichia coli (E. coli) / References: UniProt: P10026
#2: DNA chain sbmA DNA1


Mass: 8663.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA
#3: DNA chain sbmA DNA2


Mass: 8552.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA

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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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris, pH 7.0 and 17.5% PEG1000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2012
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3.1→1000 Å / Num. all: 15891 / Num. obs: 15891 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Biso Wilson estimate: 86.56 Å2 / Rmerge(I) obs: 0.087 / Χ2: 0.984 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.1-3.210.78815370.9751100
3.21-3.3490.4515520.9621100
3.34-3.4910.50.56915370.9281100
3.49-3.6814.40.41815490.9561100
3.68-3.9114.70.30515660.9531100
3.91-4.21150.16215670.9941100
4.21-4.6315.50.10515941.0121100
4.63-5.316.70.09815991.0531100
5.3-6.6818.20.07916321.0241100
6.68-100019.30.03117580.945199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.106→46.956 Å / FOM work R set: 0.811 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 764 4.83 %RANDOM
Rwork0.2237 ---
obs0.2241 15804 99.72 %-
all-15804 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.19 Å2 / Biso mean: 120.58 Å2 / Biso min: 50.43 Å2
Refinement stepCycle: LAST / Resolution: 3.106→46.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 1147 0 0 4280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034442
X-RAY DIFFRACTIONf_angle_d0.5946221
X-RAY DIFFRACTIONf_chiral_restr0.023721
X-RAY DIFFRACTIONf_plane_restr0.001605
X-RAY DIFFRACTIONf_dihedral_angle_d19.0061719
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A384X-RAY DIFFRACTIONPOSITIONAL0.006
12B384X-RAY DIFFRACTIONPOSITIONAL0.006
13C384X-RAY DIFFRACTIONPOSITIONAL0.005
14D384X-RAY DIFFRACTIONPOSITIONAL0.007
15E384X-RAY DIFFRACTIONPOSITIONAL0.005
16F384X-RAY DIFFRACTIONPOSITIONAL0.006
17G384X-RAY DIFFRACTIONPOSITIONAL0.004
18H384X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1065-3.34630.2521430.23462910305399
3.3463-3.68290.2831650.226729163081100
3.6829-4.21550.25681620.231529643126100
4.2155-5.310.24371460.229830423188100
5.31-46.96140.19881480.214432083356100
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)
13.0649-0.08050.22636.3912.8495.6083-0.38490.1812-0.2998-0.51720.65930.91081.3243-0.8565-0.29310.9437-0.2561-0.1070.9797-0.02490.4542-54.714914.5875-33.4032
25.1071-0.769-1.7042.4629-1.69724.05580.24360.24610.1672-0.81230.1728-0.360.063-0.7412-0.56010.83790.0013-0.04891.35930.0770.7412-59.409726.1029-39.1498
33.6124-1.60160.58048.0595-0.79893.44460.73070.58990.3617-1.257-0.1742-0.7629-0.4779-0.396-0.53620.720.117-0.0570.85710.26140.6851-22.272228.7756-41.5392
45.8832-1.70361.11127.40140.54453.59410.68410.218-0.498-0.9622-0.2271-0.60231.22760.342-0.45991.01770.24580.0990.79840.07090.8087-16.450517.0873-40.811
55.71850.23250.51633.1701-3.40539.9302-0.1617-0.2515-0.2232-0.08760.92430.4521.455-1.1569-0.74370.8095-0.0082-0.03580.9470.03280.6164-35.536115.3318-7.3217
64.02840.52891.13746.21580.77289.55460.2571-0.32620.06220.5749-0.4291-0.9090.24980.6065-0.05630.59690.1659-0.20091.0016-0.08760.6403-27.953826.8164-4.6632
72.35410.9631-1.33795.5154-2.14628.27340.2453-0.64941.12040.46980.22710.1306-0.74740.4946-0.32490.52130.1475-0.00950.9643-0.16070.88328.796322.8393-7.384
83.9523-1.48532.31193.7778-2.42936.70140.09580.43720.0468-0.36830.5260.24210.7393-0.1186-0.43510.70690.18260.04890.78120.00410.90684.468411.9423-14.3284
91.94050.07331.26181.2897-0.2241.0783-0.5483-0.4970.63480.1680.0687-0.208-0.0789-0.25650.39710.68130.0726-0.10641.3005-0.02461.0098-24.49727.4902-23.8091
102.02772.02041.38790.92550.6141.3018-0.46170.02570.84960.00080.1282-0.133-0.0957-0.21330.16670.630.2364-0.0621.28820.04661.0553-26.257327.4345-22.207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 51
2X-RAY DIFFRACTION2chain DD2 - 53
3X-RAY DIFFRACTION3chain BB2 - 53
4X-RAY DIFFRACTION4chain CC2 - 53
5X-RAY DIFFRACTION5chain EE2 - 51
6X-RAY DIFFRACTION6chain HH2 - 52
7X-RAY DIFFRACTION7chain FF2 - 53
8X-RAY DIFFRACTION8chain GG2 - 51
9X-RAY DIFFRACTION9chain PP1 - 28
10X-RAY DIFFRACTION10chain QQ1 - 28

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