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Basic information

Entry
Database: PDB / ID: 5ewb
TitleRacemic crystal structures of Pribnow box consensus promoter sequence (P21/c)
Components
  • PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND
  • PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.694 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 20, 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 / 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- TEMPLATE STRAND
B: PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND
C: PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND
D: PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND


Theoretical massNumber of molelcules
Total (without water)14,6504
Polymers14,6504
Non-polymers00
Water1,51384
1
A: PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND
B: PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND
D: PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.118, 67.115, 47.860
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number14
Space group name H-MP121/c1

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Components

#1: DNA chain PRIBNOW BOX CONSENSUS SEQUENCE- TEMPLATE STRAND


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Pribnow box consensus sequence TATAAT / Source: (synth.) synthetic construct (others)
#2: DNA chain PRIBNOW BOX CONSENSUS SEQUENCE- NON-TEMPLATE STRAND


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.35 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Racemic DNA mixture*, sodium cacodylate, sodium chloride, potassium chloride, spermine tetrahydrochloride, MPD *For crystallization, four strands were used i.e. (1) d(CGCTATAATGCG) with L- ...Details: Racemic DNA mixture*, sodium cacodylate, sodium chloride, potassium chloride, spermine tetrahydrochloride, MPD *For crystallization, four strands were used i.e. (1) d(CGCTATAATGCG) with L-sugars; (2) d(CGCATTATAGCG) with L-sugars; (3) d(CGCTATAATGCG) with D-sugars and (4) d(CGCATTATAGCG) with D-sugars. Enantio-pure DNA solutions were prepared between the non-self complementary strands. Enantiopure DNA solutions were mixed in equimolar ratio and this racemic mixture was used for crystallization.
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 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: 1.69→42.6 Å / Num. obs: 29346 / % possible obs: 99.3 % / Redundancy: 6.56 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.64
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 6.42 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.02 / % possible all: 97.1

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Processing

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

1fq2


Resolution: 1.694→42.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3496 1431 4.9 %Random selection
Rwork0.2988 ---
obs0.3012 29228 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.694→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 972 0 84 1056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081088
X-RAY DIFFRACTIONf_angle_d1.0121672
X-RAY DIFFRACTIONf_dihedral_angle_d32.169464
X-RAY DIFFRACTIONf_chiral_restr0.052188
X-RAY DIFFRACTIONf_plane_restr0.01148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.694-1.75460.48351270.45212679X-RAY DIFFRACTION95
1.7546-1.82480.44771500.42632763X-RAY DIFFRACTION99
1.8248-1.90790.44471430.41532794X-RAY DIFFRACTION100
1.9079-2.00850.43111490.42572787X-RAY DIFFRACTION100
2.0085-2.13430.46761540.38112780X-RAY DIFFRACTION100
2.1343-2.29910.47371300.35712824X-RAY DIFFRACTION100
2.2991-2.53040.34921740.35762778X-RAY DIFFRACTION100
2.5304-2.89650.42281310.35742817X-RAY DIFFRACTION100
2.8965-3.6490.33971420.30932762X-RAY DIFFRACTION99
3.649-42.61540.25881310.20642813X-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)
12.38240.14010.27383.4968-0.22372.9191-0.35680.13610.5486-0.4487-0.31750.481-0.435-0.39770.54750.38390.0712-0.11040.3974-0.06420.481645.23144.65528.5881
26.3926-2.28912.31527.9204-0.31822.0659-0.05760.41470.46090.4967-0.3429-0.66050.2567-0.01180.43090.40180.0060.01980.3726-0.05420.334544.067723.257617.0321
31.2453-1.17250.98542.5756-0.36610.97380.28140.318-0.2248-0.3626-0.3686-0.11640.18920.17970.10870.44250.05680.01480.3673-0.03530.364740.637224.465813.5866
40.959-1.3154-0.57728.11293.53097.97990.0566-0.08470.42570.4981-0.6462-0.0582-0.2852-0.76850.4840.38560.0643-0.09440.4253-0.00350.442847.18044.565516.2136
51.6207-0.00370.73333.36270.53072.9582-0.21350.16370.6310.1282-0.10650.3205-0.3288-0.33790.4150.32840.06170.01580.3442-0.02080.405258.82087.434132.0831
62.8336-1.14511.06835.0095-0.46953.0532-0.03320.29450.01790.3084-0.3086-0.98840.20930.19130.33740.35440.01010.10490.3912-0.03480.528858.66225.837639.4618
70.8202-0.40770.98332.5626-0.05521.24240.04030.4262-0.2991-0.6196-0.1719-0.4185-0.05120.11110.110.35370.02790.09060.3694-0.03930.385555.551827.200536.1033
84.0124-0.15740.43066.98912.4528.04240.0174-0.62280.6630.9088-0.2403-0.63240.5027-0.55860.28040.42730.0649-0.03110.3741-0.01570.418860.50926.942539.7983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 12 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 7 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 12 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 5 )
6X-RAY DIFFRACTION6chain 'C' and (resid 6 through 12 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 7 )
8X-RAY DIFFRACTION8chain 'D' and (resid 8 through 12 )

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