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- PDB-1hq7: CRYSTALLOGRAPHIC STUDIES OF A DODECAMER B-DNA D-(GCAAACGTTTGC)2 -

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Basic information

Entry
Database: PDB / ID: 1hq7
TitleCRYSTALLOGRAPHIC STUDIES OF A DODECAMER B-DNA D-(GCAAACGTTTGC)2
Components5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3'
KeywordsDNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsChen, S. / Berman, H.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Signatures of protein-DNA recognition in free DNA binding sites.
Authors: Locasale, J.W. / Napoli, A.A. / Chen, S. / Berman, H.M. / Lawson, C.L.
History
DepositionDec 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3'
B: 5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.638, 39.638, 98.591
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-67-

HOH

21B-70-

HOH

DetailsThe biological assembly is a DNA duplex

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Components

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


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid-phase DNA synthesis
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, magnesium acetate, sodium cacodylate, spermine tetrahydrochloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2magnesium acetate11
3sodium cacodylate11
4spermine tetrahydrochloride11
5MPD12
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetails
11 mMspermine tetrahydrochloride1
230 %MPD1
340 mMmagnesium acetate1
450 mMsodium cacodylate1pH6.0
51

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11081
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X8C11.0722
ROTATING ANODEOTHER21.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 4r1CCDJun 7, 2000mirrors
ADSC QUANTUM 12CCDAug 21, 2000mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1parabolic collimating mirrorSINGLE WAVELENGTHMx-ray1
2parabolic collimating mirrorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.07221
21.54181
ReflectionResolution: 2.1→13 Å / Num. all: 5576 / Num. obs: 54956 / % possible obs: 94.6 % / Observed criterion σ(F): 4 / Redundancy: 9.9 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.234 / Num. unique all: 269 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 13 Å / Num. obs: 5576 / Num. measured all: 54956

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→13 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 466472.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.266 518 9.8 %RANDOM
Rwork0.237 ---
obs0.237 5310 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.74 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å2-13.62 Å20 Å2
2---2.59 Å20 Å2
3---5.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.1→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 100 586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.1
X-RAY DIFFRACTIONc_improper_angle_d1.88
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 84 10.5 %
Rwork0.318 717 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.002
X-RAY DIFFRACTIONc_angle_deg2.07
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg0.171
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.88

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