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- PDB-1cw9: DNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE -

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Basic information

Entry
Database: PDB / ID: 1cw9
TitleDNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE
Components5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'
KeywordsDNA / CROSSLINKED DOUBLE-HELICAL DNA / BASE-PAIR OPENING / PARTIAL BASE FLIPPING.
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
Authorsvan Aalten, D.M.F. / Erlanson, D.A. / Verdine, G.L. / Joshua-Tor, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: A structural snapshot of base-pair opening in DNA.
Authors: van Aalten, D.M. / Erlanson, D.A. / Verdine, G.L. / Joshua-Tor, L.
History
DepositionAug 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 7, 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'
B: 5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'
C: 5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'
D: 5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4655
Polymers12,4244
Non-polymers401
Water4,882271
1
A: 5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'
B: 5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2523
Polymers6,2122
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'
D: 5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,2122
Polymers6,2122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.435, 43.180, 72.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain
5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3'


Mass: 3106.110 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: CROSSLINKED DNA WAS SYNTHESIZED BY THE CONVERTIBLE NUCLEOSIDE APPROACH
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.13 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, CALCIUM CHLORIDE, SODIUM CHLORIDE, SPERMINE TETRACHLORIDE, SODIUM CACODYLATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1CACL211
2NACL11
3SPERMINE11
4SODIUM CACODYLATE11
5MPD11
6MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
22.5 %MPD1drop
3100 mM1dropCaCl2
440 mM1dropNaCl
56 mMspermine tetrachloride1drop
625 mMcacodylate1drop
735 %MPD1reservoir
1DNA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.55→13 Å / Num. all: 62990 / Num. obs: 62990 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 98
Reflection
*PLUS
Num. obs: 15570 / Num. measured all: 62990
Reflection shell
*PLUS
% possible obs: 98 % / Num. unique obs: 1555

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BDJ017

Resolution: 1.55→13 Å / Isotropic thermal model: RESTRAINED CNS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: CNS NUCLEIC ACID PARAMETERS USING SOFT VAN DER WAALS PARAMETERS (PARKINSON ET AL., ACTA D, 52, 57-64 (1996)).
Details: MAXIMUM LIKELIHOOD.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 782 5 %RANDOM
Rwork0.203 ---
all0.2031 15525 --
obs0.2031 15525 95.7 %-
Solvent computationSolvent model: FLAT - CNS CALCULATED MASK
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.895 Å20 Å20 Å2
2---2.358 Å20 Å2
3----1.537 Å2
Refinement stepCycle: LAST / Resolution: 1.55→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 820 1 271 1092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.53
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_it3.938
X-RAY DIFFRACTIONc_mcangle_it4.824
X-RAY DIFFRACTIONc_scbond_it2.875
X-RAY DIFFRACTIONc_scangle_it3.828
LS refinement shellResolution: 1.55→1.61 Å / % reflection Rfree: 5 % / % reflection obs: 98 %
Xplor fileSerial no: 1 / Param file: DNA-RNA_REP.PARAM / Topol file: DNA-RNA.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 13 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.3 Å2
LS refinement shell
*PLUS
% reflection Rfree: 5 %

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