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

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Basic information

Entry
Database: PDB / ID: 4qpo
TitleMechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, TraM
ComponentsRelaxosome protein TraM
KeywordsTRANSCRIPTION / RHH Domain / DNA Binding
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
PHOSPHATE ION / Relaxosome protein TraM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.999 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 3, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4518
Polymers24,0714
Non-polymers3804
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-74 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.682, 115.682, 54.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Relaxosome protein TraM


Mass: 6017.867 Da / Num. of mol.: 4
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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M ammonium phosphate dibasic, 100 mM sodium citrate, pH 5.5 and 200 mM NaCl., VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.07808 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2014
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07808 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 18422 / Num. obs: 18422 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 35.54 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.085 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.075.30.7418431.206199.8
2.07-2.155.40.52618241.231100
2.15-2.255.50.36418771.211100
2.25-2.375.50.26618501.1611100
2.37-2.525.60.19718351.0411100
2.52-2.715.60.14118301.0051100
2.71-2.995.60.09818641.0061100
2.99-3.425.50.07518491.0051100
3.42-4.315.30.05418420.9871100
4.31-505.70.03818081.006197.9

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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
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→36.946 Å / FOM work R set: 0.8384 / SU ML: 0.19 / σ(F): 1.98 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 946 5.14 %RANDOM
Rwork0.1922 ---
obs0.1942 18416 99.76 %-
all-18416 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.33 Å2 / Biso mean: 51.14 Å2 / Biso min: 23.28 Å2
Refinement stepCycle: LAST / Resolution: 1.999→36.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 20 24 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111626
X-RAY DIFFRACTIONf_angle_d1.0822187
X-RAY DIFFRACTIONf_chiral_restr0.05253
X-RAY DIFFRACTIONf_plane_restr0.004280
X-RAY DIFFRACTIONf_dihedral_angle_d13.243597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9995-2.10490.2741620.254924912653100
2.1049-2.23670.21151220.217624982620100
2.2367-2.40940.23641260.206625232649100
2.4094-2.65180.29021270.217124982625100
2.6518-3.03540.22411400.203924972637100
3.0354-3.82360.2471350.191425022637100
3.8236-36.95240.20411340.1682461259599
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)
15.8292.6929-2.53552.3306-1.65853.46330.41080.77930.8793-0.29290.1919-0.0562-0.2420.0517-0.59460.3539-0.01070.0240.46160.06880.411511.513424.807515.9993
24.63290.3950.2827.80172.16364.5027-0.36270.5498-1.4357-1.4924-0.14860.22760.58010.21040.36830.93120.20110.15871.0941-0.16490.72418.355311.6377.1208
30.82530.71690.15293.2865-1.43210.9455-1.4943-0.6645-2.7306-0.85540.32170.89740.8886-1.69651.37830.9221-0.00130.07651.2026-0.6251.58649.52414.2527.899
46.2423-1.9743-1.58227.3946-1.91616.86110.01160.0201-1.09930.28650.19910.22570.9099-0.5201-0.10390.27280.1156-0.02830.3881-0.12870.459216.632914.077523.2569
51.98631.5943-2.12262.114-1.23976.9469-0.00660.00990.19150.01990.1224-0.15290.16870.8419-0.03680.28390.0322-0.02050.528-0.01470.263142.40773.333931.4725
66.62993.98073.51626.39713.91669.5149-0.2266-0.6240.1680.0594-0.22640.38230.5166-0.25540.3610.21950.00490.02150.2947-0.00680.310827.6005-5.845130.9793
78.57473.81031.56373.5115-0.37325.48350.14060.0588-0.4624-0.6340.0731-0.00760.84550.0367-0.08850.5974-0.00360.01980.30650.00620.348729.6909-12.183521.1898
85.6638-1.8524-0.49017.52880.5384.6070.03330.06910.6877-0.6245-0.2612-0.0459-0.161-0.23660.17530.21980.0541-0.00630.303-0.01150.300132.56057.232923.8252
93.898-0.3825-3.18943.8391-1.44624.59450.65312.09180.5257-0.78010.25190.7831-0.29270.7121-0.49450.3177-0.2356-0.13110.82130.21440.56668.023421.433716.1919
106.33591.29052.14976.05310.96114.4878-0.059-0.34050.87070.3043-0.07990.6246-0.4961-0.36580.0760.3350.07540.02130.3958-0.03520.354615.094426.949830.8603
115.2485-2.4616-1.05569.10040.56675.00980.1990.8931-0.408-1.1221-0.4014-0.45840.34-0.04360.19590.40130.08920.02440.4984-0.06410.318620.789916.270218.9839
120.35230.227-1.11010.53960.09375.4005-0.1245-0.2117-0.0786-0.19970.031-0.2520.55830.37190.10270.39620.0945-0.00580.4438-0.01530.306742.8231.016327.098
132.82990.00550.39243.90455.40868.30840.16790.39480.2386-1.09520.1574-1.221-1.00770.0009-0.22480.45170.00320.07340.4207-0.00610.405742.580818.359624.7116
142.4877-0.1473-0.04286.15390.46381.94060.0816-0.6424-0.0174-0.0077-0.1268-0.1958-0.0674-0.10880.03040.25330.06410.01990.2928-0.06070.242335.333611.205431.6606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 9 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 25 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 34 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 35 through 54 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 9 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 25 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 34 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 35 through 52 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 9 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 10 through 34 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 35 through 54 )C0
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 9 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 10 through 26 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 27 through 53 )D0

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