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- PDB-5f26: Crystal structures of Pribnow box consensus promoter sequence (P63) -

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Basic information

Entry
Database: PDB / ID: 5f26
TitleCrystal structures of Pribnow box consensus promoter sequence (P63)
Components
  • Complementary strand
  • Pribnow box consensus sequence strand
KeywordsDNA / Racemic DNA crystallography / Pribnow box / Bacterial Promoter / B-DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMandal, P.K. / Collie, G.W. / Kauffmann, B. / Srivastava, S.C. / Huc, I.
Funding support France, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-320892 France
Citation
Journal: Nucleic Acids Res. / Year: 2016
Title: Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography.
Authors: Mandal, P.K. / Collie, G.W. / Srivastava, S.C. / Kauffmann, B. / Huc, I.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pribnow box consensus sequence strand
B: Complementary strand


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-2 kcal/mol
Surface area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.232, 49.232, 67.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: DNA chain Pribnow box consensus sequence strand


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Pribnow box consensus sequence TATAAT / Source: (synth.) synthetic construct (others)
#2: DNA chain Complementary strand


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.62 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: DNA, sodium cacodylate, barium chloride, potassium chloride, spermine tetrahydrochloride, 2-methyl-2,4-pentanediol
PH range: 7

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→42.64 Å / Num. obs: 2101 / % possible obs: 99.6 % / Redundancy: 1.93 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 16.94
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 1.78 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 463D

463d


Resolution: 3→36.074 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 192 5.36 %Random selection
Rwork0.2885 ---
obs0.289 1857 97.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→36.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 448 0 5 453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005501
X-RAY DIFFRACTIONf_angle_d0.72769
X-RAY DIFFRACTIONf_dihedral_angle_d31.817213
X-RAY DIFFRACTIONf_chiral_restr0.03287
X-RAY DIFFRACTIONf_plane_restr0.00322
LS refinement shellResolution: 3.0004→36.0771 Å
RfactorNum. reflection% reflection
Rfree0.2983 192 -
Rwork0.2885 3393 -
obs--97 %
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)
10.0408-0.01670.02430.0006-0.01690.1601-0.04450.0892-0.0558-0.19640.0440.1199-0.23280.1035-0.00750.10940.0107-0.19950.23910.19790.357749.743311.8404-9.2497
20.0301-0.0078-0.0312-0.01790.02320.0564-0.16070.15520.07620.1266-0.0795-0.2092-0.10.0179-0.2332-0.44480.12520.24220.2118-0.4833-1.074649.49911.552711.8286
30.08550.009-0.04430.0006-0.03430.0757-0.1775-0.0343-0.00610.0459-0.16610.0190.00030.0383-0.2320.1599-0.250.4539-0.19770.5827-0.203843.102712.18049.6783
40.153-0.11580.09290.0992-0.03860.0787-0.1512-0.0536-0.169-0.0379-0.1513-0.22630.0144-0.0564-0.04090.3714-0.4710.29090.58790.05620.35857.42518.9415-3.8547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 12 )
3X-RAY DIFFRACTION3chain 'B' and (resid 14 through 18 )
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 23 )

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