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- PDB-1en9: 1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING A... -

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Basic information

Entry
Database: PDB / ID: 1en9
Title1A 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*GP*CP*GP*CP*TP*GP*G)-3')
KeywordsDNA / divalent cations / DNA sequence-specific binding / shelxdna / B-DNA
Function / homologyDNA
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_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*GP*CP*GP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1927
Polymers3,0461
Non-polymers1466
Water1,42379
1
A: DNA (5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,38414
Polymers6,0922
Non-polymers29212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)32.243, 25.352, 34.190
Angle α, β, γ (deg.)90.00, 117.17, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-111-

MG

21A-228-

HOH

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Components

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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.06 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop
Details: initial concentration in droplet: 0.17 mM dna, 31.40 mM magnesium acetate 0.28 mM streptonigrin, 10-15% MPD, 30% final MPD concentration in reservoir. Solutions were unbuffered, VAPOR ...Details: initial concentration in droplet: 0.17 mM dna, 31.40 mM magnesium acetate 0.28 mM streptonigrin, 10-15% MPD, 30% final MPD concentration in reservoir. Solutions were unbuffered, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium acetate11
2streptonigrin11
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.17 mMduplex DNA1drop
231.40 mMdivalent cation1drop
30.28 mMstreptonigrin1drop
430 %1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / 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: 13087 / Num. obs: 13087 / % possible obs: 93.3 % / Observed criterion σ(I): -1 / Redundancy: 4.87 % / Biso Wilson estimate: 5.82 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 32.8
Reflection shellResolution: 0.985→1.016 Å / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1253 / % possible all: 89.5
Reflection
*PLUS
Num. measured all: 63745
Reflection shell
*PLUS
% possible obs: 89.5 %

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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: 16139 / Num. restraintsaints: 5024 / 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
Rfree0.1509 654 5 %random
Rwork0.1405 ---
obs0.1405 13087 93.3 %-
all-13087 --
Solvent computationSolvent model: SHELX swat option
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 113 / Occupancy sum non hydrogen: 271.4
Refinement stepCycle: LAST / Resolution: 0.985→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 385 48 51 484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.041
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.023
X-RAY DIFFRACTIONs_approx_iso_adps0.039
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg3.61
LS refinement shell
*PLUS
Rfactor Rfree: 0.184 / Rfactor Rwork: 0.1653

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