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- PDB-1jes: Crystal Structure of a Copper-Mediated Base Pair in DNA -

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Entry
Database: PDB / ID: 1jes
TitleCrystal Structure of a Copper-Mediated Base Pair in DNA
Components5'-D(*CP*GP*CP*GP*(DPY)P*AP*TP*(DRP)P*CP*GP*CP*G)-3'
KeywordsDNA / Cu / copper / Z-DNA / dodecamer / duplex / unnatural / designed
Function / homologyCOPPER (II) ION / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsAtwell, S. / Meggers, E. / Spraggon, G. / Schultz, P.G.
Citation
Journal: J.Am.Chem.Soc. / Year: 2001
Title: Structure of a Copper-Mediated Base Pair in DNA
Authors: Atwell, S. / Meggers, E. / Spraggon, G. / Schultz, P.G.
#1: Journal: J.Am.Chem.Soc. / Year: 2000
Title: A Novel Copper-Mediated DNA Base Pair
Authors: Meggers, E. / Holland, P.L. / Tolman, W.B. / Romesberg, F.E. / Schultz, P.G.
#2: Journal: Science / Year: 1981
Title: Left-handed double helical DNA: variations in the backbone conformation
Authors: Wang, A.G.-J. / Quigley, G.J. / Kolpak, F.J. / van Der Marel, G. / van Boom, J.H. / Rich, A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Structure of a B-DNA dodecamer: conformation and dynamics
Authors: Drew, H.R. / Wing, R.M. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E.
History
DepositionJun 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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_conn_type / 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_conn_type.id / _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*GP*(DPY)P*AP*TP*(DRP)P*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*(DPY)P*AP*TP*(DRP)P*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4244
Polymers7,2972
Non-polymers1272
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.343, 34.359, 31.093
Angle α, β, γ (deg.)90.00, 101.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3648.371 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.82 Å3/Da / Density % sol: 32.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% MPD, 40 mM Na Cacodylate, 12 mM Spermine tetra-HCl, 80 mM NaCl, 20 mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Na Cacodylate11
3Spermine tetra-HCl11
4NaCl11
5MgCl211

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.37991,1.37791,1.0
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2001 / Details: Curved Si (111)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.379911
21.377911
311
ReflectionResolution: 1.5→50 Å / Num. all: 47272 / Num. obs: 47190 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 14.058 Å2 / Rsym value: 0.096 / Net I/σ(I): 46.7
Reflection shellResolution: 1.49→1.54 Å / Rmerge(I) obs: 0.686 / % possible all: 84.1
Reflection
*PLUS
Num. obs: 8531 / Num. measured all: 47272 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 84.1 % / Rmerge(I) obs: 0.686

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: initial map fit with mononucleotides

Resolution: 1.5→50 Å / Cross valid method: free r / σ(F): 0 / σ(I): 0
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996).
Details: The fofc maps indicated an alternate conformation for the phosphate of B23, and so the structure was refined with two conformations for the phosphate of B23 (excepting the O5') and most of ...Details: The fofc maps indicated an alternate conformation for the phosphate of B23, and so the structure was refined with two conformations for the phosphate of B23 (excepting the O5') and most of residue B22 (excepting O5'), each with 0.5 occupancy.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 682 8 %Random 8%
Rwork0.169 ---
all-8520 --
obs-8520 98 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.399 Å20 Å2-0.784 Å2
2---0.007 Å20 Å2
3---0.406 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 505 2 82 589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00893
X-RAY DIFFRACTIONc_angle_deg1.56
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. reflection obs: 8531 / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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