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- PDB-3u89: Crystal structure of one turn of g/c rich b-dna revisited -

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Basic information

Entry
Database: PDB / ID: 3u89
TitleCrystal structure of one turn of g/c rich b-dna revisited
Components5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G) -3'
KeywordsDNA / B-DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsMaehigashi, T. / Woods, K.K. / Moulaei, T. / Komeda, S. / Williams, L.D.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: B-DNA structure is intrinsically polymorphic: even at the level of base pair positions.
Authors: Maehigashi, T. / Hsiao, C. / Woods, K.K. / Moulaei, T. / Hud, N.V. / Williams, L.D.
History
DepositionOct 16, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionNov 9, 2011ID: 3GGB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,1686
Polymers3,0461
Non-polymers1225
Water2,018112
1
A: 5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G) -3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,33512
Polymers6,0922
Non-polymers24310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1500 Å2
ΔGint-41 kcal/mol
Surface area4020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.136, 25.172, 34.094
Angle α, β, γ (deg.)90.00, 116.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-25-

MG

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Components

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


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium Cacodylate, Magnesium Acetate, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2003
RadiationMonochromator: Cryogenically cooled Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.91→30.6 Å / Num. obs: 14269 / % possible obs: 80.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 53.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BD1

1bd1


Resolution: 0.96→16.06 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.44 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12487 1087 7.8 %RANDOM
Rwork0.10291 ---
obs0.10463 12848 92.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.412 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.17 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 0.96→16.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 5 112 319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021376
X-RAY DIFFRACTIONr_angle_refined_deg1.9843640
X-RAY DIFFRACTIONr_chiral_restr0.1220.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0340.02126
X-RAY DIFFRACTIONr_scbond_it1.8653376
X-RAY DIFFRACTIONr_scangle_it2.4924.5638
X-RAY DIFFRACTIONr_rigid_bond_restr1.0913376
LS refinement shellResolution: 0.96→0.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 48 -
Rwork0.162 504 -
obs--50.18 %

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