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- PDB-1s23: Crystal Structure Analysis of the B-DNA Decamer CGCAATTGCG -

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Entry
Database: PDB / ID: 1s23
TitleCrystal Structure Analysis of the B-DNA Decamer CGCAATTGCG
Components5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3'
KeywordsDNA / deoxyoligonucleotide / cobalt / variability
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsValls, N. / Wright, G. / Steiner, R.A. / Murshudov, G.N. / Subirana, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: DNA variability in five crystal structures of d(CGCAATTGCG).
Authors: Valls, N. / Wright, G. / Steiner, R.A. / Murshudov, G.N. / Subirana, J.A.
History
DepositionJan 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_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_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.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_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_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
Revision 1.4Apr 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*GP*CP*AP*AP*TP*TP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1042
Polymers3,0451
Non-polymers591
Water82946
1
A: 5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,2084
Polymers6,0902
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_575x,-y+2,-z+1/21
Unit cell
Length a, b, c (Å)26.220, 44.359, 52.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-300-

CO

21A-322-

HOH

31A-323-

HOH

41A-334-

HOH

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Components

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


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.56 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, acridine(RGR), cacodylate, calcium chloride, cobalt chloride, spermine , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2acridine(RGR)11
3cacodylate11
4calcium chloride11
5cobalt chloride11
6spermine11
7MPD12
8calcium chloride12
9cobalt chloride12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.917 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. obs: 4174 / % possible obs: 98.4 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.061 / Rsym value: 0.077
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.93 / Num. unique all: 376 / Rsym value: 0.6 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY UDJ031

Resolution: 1.6→22.59 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.747 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28152 414 10 %RANDOM
Rwork0.20969 ---
all0.214 ---
obs0.21601 3746 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.833 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--2.26 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 211 1 47 259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021238
X-RAY DIFFRACTIONr_bond_other_d0.0010.02101
X-RAY DIFFRACTIONr_angle_refined_deg2.5953369
X-RAY DIFFRACTIONr_angle_other_deg1.4313258
X-RAY DIFFRACTIONr_chiral_restr0.0820.233
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02117
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022
X-RAY DIFFRACTIONr_nbd_refined0.130.220
X-RAY DIFFRACTIONr_nbd_other0.190.2102
X-RAY DIFFRACTIONr_nbtor_other0.0980.251
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3540.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.216
X-RAY DIFFRACTIONr_scbond_it2.3053238
X-RAY DIFFRACTIONr_scangle_it3.3874.5369
LS refinement shellResolution: 1.6→1.644 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.416 26
Rwork0.459 221

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