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

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Basic information

Entry
Database: PDB / ID: 5ezf
TitleRacemic crystal structures of Pribnow box consensus promoter sequence (Pbca)
Components
  • Complementary strand
  • Pribnow box template strand
KeywordsDNA / Pribnow box consensus sequence / -10 element / transcription initiation / B-DNA double helix / DNA double helix
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 26, 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 ...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_asym_id / _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.ptnr3_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 template strand
B: Complementary strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4054
Polymers7,3252
Non-polymers802
Water93752
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-18 kcal/mol
Surface area4560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.736, 39.329, 65.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number61
Space group name H-MPbca

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.85 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Racemic DNA mixture*, HEPES, calcium chloride, PEG400 * For crystallization, we used four strands 1) d(CGCTATAATGCG) with L-sugars 2) d(CGCATTATAGCG) with L-sugars and 3) d(CGCTATAATGCG) ...Details: Racemic DNA mixture*, HEPES, calcium chloride, PEG400 * 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 DNA solutions were prepared first by de-naturation followed by slow cooling down process to ensure proper folding of the hetero-duplex formed between the non-self complementary strands. After slow-annealing, the enantiopure solutions were mixed in equimolar ratio and this racemic DNA mixture was used for crystallization.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 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: 1.65→32.86 Å / Num. obs: 12549 / % possible obs: 99.86 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.019 / Net I/σ(I): 16.92
Reflection shellResolution: 1.65→1.79 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.75 / % possible all: 99.76

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FQ2

1fq2


Resolution: 1.65→32.856 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3167 611 4.87 %Random selection
Rwork0.2963 ---
obs0.2973 12548 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→32.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 2 52 540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007544
X-RAY DIFFRACTIONf_angle_d1.626836
X-RAY DIFFRACTIONf_dihedral_angle_d32.069232
X-RAY DIFFRACTIONf_chiral_restr0.05494
X-RAY DIFFRACTIONf_plane_restr0.00724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.8160.47861600.39542976X-RAY DIFFRACTION100
1.816-2.07880.40181480.39092987X-RAY DIFFRACTION100
2.0788-2.61890.4311520.37732994X-RAY DIFFRACTION100
2.6189-32.8630.26231510.25152980X-RAY DIFFRACTION100
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)
1-0.48840.2976-0.5697-1.7710.24170.60090.2168-0.09610.1069-0.03050.2131-0.00640.05430.18550.06190.39140.0140.01750.3040.00240.2524-6.5817-1.637618.743
2-0.64931.2877-0.6239-1.0815-0.45580.37920.324-0.1166-0.1001-0.02250.1040.2642-0.17930.52350.08420.34720.04270.02490.37860.03270.312-7.6473-2.483418.3238
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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