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- PDB-1en8: 1 A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING ... -

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Basic information

Entry
Database: PDB / ID: 1en8
Title1 A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM
ComponentsDNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
KeywordsDNA / divalent cations / DNA sequence-specific binding / shelxdna / B-DNA
Function / homologyETHANOL / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.985 Å
AuthorsChiu, T.K. / Dickerson, R.E.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium.
Authors: Chiu, T.K. / Dickerson, R.E.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG.
Authors: Chiu, T.K. / Kaczor-Grzeskowiak, M. / Dickerson, R.E.
History
DepositionMar 20, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_alt_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3909
Polymers3,0451
Non-polymers3458
Water1,44180
1
A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,77918
Polymers6,0902
Non-polymers68916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)31.847, 25.100, 34.144
Angle α, β, γ (deg.)90.00, 114.87, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')


Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.02 Å3/Da / Density % sol: 36.96 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop
Details: initial concentration in droplet: 0.24 mM dna, 8.57 mM calcium acetate, 0.11 mM streptonigrin, 10-15% MPD, 45% final MPD concentration in reservoir. Solutions were unbuffered, VAPOR ...Details: initial concentration in droplet: 0.24 mM dna, 8.57 mM calcium acetate, 0.11 mM streptonigrin, 10-15% MPD, 45% final MPD concentration in reservoir. Solutions were unbuffered, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1calcium acetate11
2streptonigrin11
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.24 mMduplex DNA1drop
28.57 mMdivalent cation1drop
30.11 mMstreptonigrin1drop
445 %1reservoir
50.24 mMspermine-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 0.985→8 Å / Num. all: 13619 / Num. obs: 13619 / % possible obs: 97.5 % / Observed criterion σ(I): -1 / Redundancy: 5.56 % / Biso Wilson estimate: 5.54 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 25
Reflection shellResolution: 0.985→1.016 Å / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 9.1 / Num. unique all: 1322 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 75660
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BDJ019

Resolution: 0.985→8 Å / Num. parameters: 19026 / Num. restraintsaints: 5407 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Parkinson et al.
Details: REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT ...Details: REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT LEAST-SQUARES IN SHELXL-97. THE TOP 50 MOST DISAGREEABLE REFLECTIONS WERE REJECTED TOWARDS THE LATTER STAGES OF REFINEMENT BUT THESE ARE STILL INCLUDED IN THE RELEASED DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.1405 676 5 %random
Rwork0.1183 ---
all-13619 --
obs-13619 97.5 %-
Solvent computationSolvent model: swat 0.70325 0.7673
Refine analyzeNum. disordered residues: 22 / Occupancy sum hydrogen: 113 / Occupancy sum non hydrogen: 270.8
Refinement stepCycle: LAST / Resolution: 0.985→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 417 29 80 526
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.06
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.008
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.019
X-RAY DIFFRACTIONs_approx_iso_adps0.063
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.1966 / Rfactor Rwork: 0.129

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