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- PDB-1ngt: The Role of Minor Groove Functional Groups in DNA Hydration -

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Basic information

Entry
Database: PDB / ID: 1ngt
TitleThe Role of Minor Groove Functional Groups in DNA Hydration
Components5'-D(*CP*GP*CP*GP*AP*AP*(MTR)P*TP*CP*GP*CP*G)-3'
KeywordsDNA / spine of hydration / DNA conformation / modified base
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsWoods, K.K. / Lan, T. / McLaughlin, L.W. / Williams, L.D.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: The Role of Minor Groove Functional Groups in DNA Hydration
Authors: Woods, K.K. / Lan, T. / McLaughlin, L.W. / Williams, L.D.
History
DepositionDec 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Feb 14, 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_conn_type / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3173
Polymers7,2932
Non-polymers241
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.170, 41.050, 65.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3646.405 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium cacodylate, MPD, magnesium chloride, spermine tetrahydrochloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2MPD11
3magnesium chloride11
4spermine tetrahydrochloride11
5sodium cacodylate12
6MPD12
7magnesium chloride12
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.9 mMprotein1drop
231 mMsodium cacodylate1droppH6.5
319 mM1dropMgCl2
46.9 %MPD1drop
54.9 mMspermine tetrahydrochloride1drop
640 %1reservoir
71

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Data collection

DiffractionMean temperature: 163 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 0.7107 Å
DetectorType: SIEMENS / Detector: CCD / Date: Jan 1, 2000
RadiationMonochromator: 0.7107 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7107 Å / Relative weight: 1
ReflectionResolution: 2.04→10 Å / Num. all: 4927 / Num. obs: 4393 / Observed criterion σ(F): 3 / Observed criterion σ(I): 0
Reflection shellResolution: 2.04→2.11 Å / % possible all: 74
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 30312 / Rmerge(I) obs: 0.084

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Processing

Software
NameClassification
SAINTdata reduction
CNSrefinement
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→10 Å / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.281 -10 %random
Rwork0.207 ---
all0.223 4393 --
obs0.223 4393 --
Refinement stepCycle: LAST / Resolution: 2.04→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 7 76 567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0086
X-RAY DIFFRACTIONc_angle_deg1.2246
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection Rfree: 378 / % reflection Rfree: 22.34 % / Rfactor Rfree: 0.2815 / Rfactor Rwork: 0.2067
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.22

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