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- PDB-5et9: Racemic crystal structures of Pribnow box consensus promoter sequ... -

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Basic information

Entry
Database: PDB / ID: 5et9
TitleRacemic crystal structures of Pribnow box consensus promoter sequence (P21/n)
Components
  • Pribnow box consensus sequence- template strand
  • Pribnow box non-template strand
KeywordsDNA / Racemic DNA crystallography / Pribnow box / Bacterial Promoter / B-DNA
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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
CitationJournal: 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 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jan 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_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_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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Pribnow box consensus sequence- template strand
B: Pribnow box non-template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5994
Polymers7,3252
Non-polymers2752
Water23413
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-16 kcal/mol
Surface area4610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.786, 68.288, 34.213
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number14
Space group name H-MP121/n1

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Components

#1: DNA chain Pribnow box consensus sequence- template 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 Pribnow box non-template strand


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: DNA containing D- and L- sugars (racemic mixture), sodium cacodylate, barium chloride, potassium chloride, spermine tetrachloride, MPD
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.83→34.14 Å / Num. obs: 10610 / % possible obs: 92.16 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.016 / Net I/σ(I): 17.5
Reflection shellResolution: 1.83→1.895 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.87 / % possible all: 65.75

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1FQ2

1fq2


Resolution: 1.83→34.14 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3294 497 4.69 %
Rwork0.2978 --
obs0.2993 10599 92.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 2 13 501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01544
X-RAY DIFFRACTIONf_angle_d1.073836
X-RAY DIFFRACTIONf_dihedral_angle_d32.821232
X-RAY DIFFRACTIONf_chiral_restr0.04794
X-RAY DIFFRACTIONf_plane_restr0.0124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8302-2.01430.53551110.47812218X-RAY DIFFRACTION80
2.0143-2.30570.50281340.42922664X-RAY DIFFRACTION97
2.3057-2.90480.5041210.39712648X-RAY DIFFRACTION97
2.9048-34.14990.25611310.24322572X-RAY DIFFRACTION94
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)
1-1.6789-0.3111-1.29381.69221.443-0.20520.16570.30310.12810.44320.04530.05950.1596-0.08310.07240.52110.0140.04190.4054-0.08840.537610.923685.21817.7445
2-1.51120.40541.18672.02281.1536-0.36150.1986-0.242-0.0355-0.4137-0.0589-0.0929-0.1077-0.07910.03540.52670.0031-0.01940.3881-0.0840.505310.911985.49299.4029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 12 )

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