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- PDB-1qph: CRYSTAL STRUCTURE OF THE A-DNA DODECAMER GACCACGTGGTC -

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Entry
Database: PDB / ID: 1qph
TitleCRYSTAL STRUCTURE OF THE A-DNA DODECAMER GACCACGTGGTC
Components5'-D(P*GP*AP*CP*CP*AP*CP*GP*TP*GP*GP*TP*CP)-3'
KeywordsDNA / DOUBLE HELIX / A-DNA / MAX PROTEIN / DNA CURVATURE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / RIGID BODY REFINEMENT / Resolution: 2.5 Å
AuthorsRaaijmakers, H. / Suck, D. / Mayer, C.
CitationJournal: To be Published
Title: Crystal Structure Analysis of the A-DNA Dodecamer GACCACGTGGTC
Authors: Raaijmakers, H. / Suck, D. / Mayer, C.
History
DepositionMay 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 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: 5'-D(P*GP*AP*CP*CP*AP*CP*GP*TP*GP*GP*TP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)3,6631
Polymers3,6631
Non-polymers00
Water81145
1
A: 5'-D(P*GP*AP*CP*CP*AP*CP*GP*TP*GP*GP*TP*CP)-3'

A: 5'-D(P*GP*AP*CP*CP*AP*CP*GP*TP*GP*GP*TP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Unit cell
Length a, b, c (Å)46.300, 46.300, 72.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-46-

HOH

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Components

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


Mass: 3663.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RECOGNITION SEQUENCE OF MAX PROTEIN
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: (NH4)2SO4, WATER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2(NH4)2SO412

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→23 Å / Num. all: 1781 / Num. obs: 1781 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 43.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MAR345data collection
AUTOMARdata reduction
X-PLORphasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: NDB ID ADL045

Resolution: 2.5→7 Å / σ(F): 2
Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING STRUCTURES, ACTA CRYST. D, 52, 57-64 (1996).
Details: SIMULATED ANNEALING REFINEMENT
RfactorNum. reflection% reflection
Rwork0.225 --
obs0.225 1682 97.9 %
all-1719 -
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 247 0 45 292
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.289 206 -
obs--97.1 %
Xplor fileSerial no: 1 / Param file: PARAM_NDBX3.DNA / Topol file: TOP_NDBX3.DNA

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