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- PDB-5eyq: Racemic crystal structures of Pribnow box consensus promoter sequ... -

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Basic information

Entry
Database: PDB / ID: 5eyq
TitleRacemic crystal structures of Pribnow box consensus promoter sequence (Pnna)
Components
  • Complementary strand
  • Pribnow box template strand
KeywordsDNA / Pribnow box consensus sequence / -10 element / transcription initiation / B-DNA double helix
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionNov 25, 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 1.3Nov 21, 2018Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.4Jan 10, 2024Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pribnow box template strand
B: Complementary strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3483
Polymers7,3252
Non-polymers231
Water34219
1
A: Pribnow box template strand
B: Complementary strand
hetero molecules

A: Pribnow box template strand
B: Complementary strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6966
Polymers14,6504
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y+1/2,-z+5/21
Unit cell
Length a, b, c (Å)28.905, 68.454, 34.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number52
Space group name H-MPnna
Components on special symmetry positions
IDModelComponents
11B-101-

NA

21A-102-

HOH

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Components

#1: DNA chain Pribnow box template strand


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.32 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Racemic DNA solution*, sodium cacodylate, magnesium chloride, sodium chloride, spermine tetrahydrochloride, MPD *For crystallization, we used four strands (1) d(CGCTATAATGCG) with L-sugars ...Details: Racemic DNA solution*, sodium cacodylate, magnesium chloride, sodium chloride, spermine tetrahydrochloride, MPD *For crystallization, we used four strands (1) d(CGCTATAATGCG) with L-sugars (2) d(CGCATTATAGCG) with L-sugars and (3) d(CGCTATAATGCG) with D-sugars (4) d(CGCATTATAGCG) with D-sugars Enantio-pure L-DNA solution (strands 1,2) and D-DNA solution (strands 3,4) were prepared first with denaturation followed by slow annealing process to ensure proper folding of the duplex formed between the non-self complementary strands. After annealing, the enantiopure solutions were mixed in equimolar ratio and this racemic mixture was used for crystallization.

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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: Apr 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→34.23 Å / Num. obs: 2825 / % possible obs: 96.61 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 8.87
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 1.34 / % possible all: 78.57

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BNA

1bna


Resolution: 2.3→34.23 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.534 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35745 147 5.2 %RANDOM
Rwork0.27162 ---
obs0.27591 2678 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.461 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20 Å2
2---6.83 Å2-0 Å2
3---4.65 Å2
Refinement stepCycle: 1 / Resolution: 2.3→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 1 19 506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.011544
X-RAY DIFFRACTIONr_bond_other_d00.02272
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.17836
X-RAY DIFFRACTIONr_angle_other_deg1.63644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02284
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02116
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5093.833544
X-RAY DIFFRACTIONr_scbond_other4.5133.835543
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1875.799837
X-RAY DIFFRACTIONr_long_range_B_refined8.30732.781600
X-RAY DIFFRACTIONr_long_range_B_other8.19732.612596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.715 7 -
Rwork0.508 161 -
obs--75.34 %

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