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- PDB-477d: CALCIUM FORM OF THE B-DNA DODECAMER GGCGAATTCGCG -

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Entry
Database: PDB / ID: 477d
TitleCALCIUM FORM OF THE B-DNA DODECAMER GGCGAATTCGCG
Components5'-D(*GP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
KeywordsDNA / B-DNA DODECAMER / CALCIUM FORM
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsMinasov, G. / Tereshko, V. / Egli, M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing.
Authors: Minasov, G. / Tereshko, V. / Egli, M.
History
DepositionJun 25, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 19, 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 1.4Feb 28, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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(*GP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
B: 5'-D(*GP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5676
Polymers7,4072
Non-polymers1604
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.990, 41.990, 99.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-120-

CA

21A-243-

HOH

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Components

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


Mass: 3703.416 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: SITTING DROPS CONTAIN 1.0 MM SINGLE STRAND OLIGONUCLEOTIDE,20 MM SODIUM CACODYLATE BUFFER PH 6.9, 10-40 MM CALCIUM CLORIDE,AGAINST RESERVOIR OF 40% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2CACL211
3MPD12
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
10.8-1.2 mMDNA single strand1
210-40 mM1CaCl2
340 %11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.99503
DetectorType: MARRESEARCH / Detector: CCD / Date: May 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99503 Å / Relative weight: 1
ReflectionResolution: 1.7→23 Å / Num. all: 7036 / Num. obs: 7036 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.346 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 39012 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 642 10 %RANDOM
Rwork0.194 ---
obs0.194 6228 86.3 %-
all-6230 --
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 456 4 151 611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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