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- PDB-5j0e: Crystal structures of Pribnow box consensus promoter sequence (P32) -

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Basic information

Entry
Database: PDB / ID: 5j0e
TitleCrystal structures of Pribnow box consensus promoter sequence (P32)
Components
  • Complementary sequence
  • Pribnow box consensus promoter sequence
KeywordsDNA / Pribnow box / consensus promoter-sequence / Racemic DNA / DNA crystallography
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsMandal, P.K. / Collie, G.W. / Kauffmann, B. / 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
DepositionMar 28, 2016Deposition 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_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.ptnr2_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.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_label_seq_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 promoter sequence
B: Complementary sequence
C: Pribnow box consensus promoter sequence
D: Complementary sequence
E: Pribnow box consensus promoter sequence
F: Complementary sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,68315
Polymers22,0946
Non-polymers5899
Water1,29772
1
A: Pribnow box consensus promoter sequence
B: Complementary sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5615
Polymers7,3652
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-60 kcal/mol
Surface area4470 Å2
MethodPISA
2
C: Pribnow box consensus promoter sequence
D: Complementary sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5615
Polymers7,3652
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-58 kcal/mol
Surface area4480 Å2
MethodPISA
3
E: Pribnow box consensus promoter sequence
F: Complementary sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5615
Polymers7,3652
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-56 kcal/mol
Surface area4480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.906, 46.906, 99.044
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: DNA chain Pribnow box consensus promoter sequence


Mass: 3662.404 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: This dodecanucleotide sequence contains the Pribnow box consensus promoter sequence TATAAT at the centre
Source: (synth.) synthetic construct (others)
#2: DNA chain Complementary sequence


Mass: 3702.428 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MPD, sodium cacodylate, zinc chloride, spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5417 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.507
11K, H, -L20.493
ReflectionResolution: 2.81→40.62 Å / Num. obs: 5955 / % possible obs: 99.3 % / Redundancy: 1.98 % / Rmerge(I) obs: 0.0283 / Rsym value: 0.0369 / Net I/σ(I): 17.08
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 1.91 % / Rmerge(I) obs: 0.1357 / Mean I/σ(I) obs: 3.87 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 463D

463d


Resolution: 2.81→40.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 12.066 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24801 319 5.4 %RANDOM
Rwork0.22587 ---
obs0.22707 5584 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.455 Å2
Baniso -1Baniso -2Baniso -3
1-14.21 Å2-0 Å20 Å2
2--14.21 Å20 Å2
3----28.43 Å2
Refinement stepCycle: 1 / Resolution: 2.81→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1362 9 72 1443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0111524
X-RAY DIFFRACTIONr_bond_other_d0.0040.02744
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.1762340
X-RAY DIFFRACTIONr_angle_other_deg1.74831770
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_restr0.0860.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02798
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02324
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_it4.044.3911524
X-RAY DIFFRACTIONr_scbond_other4.0424.3911523
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5926.572341
X-RAY DIFFRACTIONr_long_range_B_refined10.26342.8186528
X-RAY DIFFRACTIONr_long_range_B_other10.21642.9726496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.806→2.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.577 21 -
Rwork0.32 394 -
obs--93.05 %

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