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- PDB-1m77: Near Atomic Resolution Crystal Structure of an A-DNA Decamer d(CC... -

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Entry
Database: PDB / ID: 1m77
TitleNear Atomic Resolution Crystal Structure of an A-DNA Decamer d(CCCGATCGGG): Cobalt Hexammine Interactions with A-DNA
Components5'-D(*CP*CP*CP*GP*AP*TP*CP*GP*GP*G)-3'
KeywordsDNA / A-DNA / Cobalt hexammine
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsRamakrishnan, B. / Sekharudu, C. / Pan, B.C. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNA.
Authors: Ramakrishnan, B. / Sekharudu, C. / Pan, B. / Sundaralingam, M.
History
DepositionJul 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 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(*CP*CP*CP*GP*AP*TP*CP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2072
Polymers3,0461
Non-polymers1611
Water61334
1
A: 5'-D(*CP*CP*CP*GP*AP*TP*CP*GP*GP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,4144
Polymers6,0922
Non-polymers3222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)44.3, 44.3, 24.8
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: cobalt hexammine, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1cobalt hexammine11
2cacodylateCacodylic acid11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMDNA single strand1drop
240 mMsodium cacodylate1droppH6.0
30.5 mMcobalt hexammine chloride1drop
450 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: NICOLET / Detector: AREA DETECTOR / Date: Sep 22, 1993 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.25→28 Å / Num. all: 7785 / Num. obs: 6929 / % possible obs: 90 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Rsym value: 0.055
Reflection shellResolution: 1.25→1.31 Å / Num. unique all: 433
Reflection
*PLUS
% possible obs: 90 % / Num. measured all: 51067 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
X-GEN2data scaling
X-GEN2data reduction
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fiber A-DNA

Resolution: 1.25→8 Å / Isotropic thermal model: isotropic / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.185 653 random
Rwork0.163 --
all-5969 -
obs-5316 -
Refinement stepCycle: LAST / Resolution: 1.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 7 34 243
LS refinement shellResolution: 1.25→1.31 Å /
RfactorNum. reflection
Rfree0.224 52
Rwork0.197 -
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg3.4

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