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- PDB-4xqz: Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), ... -

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Basic information

Entry
Database: PDB / ID: 4xqz
TitleCalcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), complexed by chloride and MES
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / copper(II)
Function / homologyCOPPER (II) ION / METHANOL / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsRohner, M. / Medina-Molner, A. / Spingler, B.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Inorg.Chem. / Year: 2016
Title: N,N,O and N,O,N Meridional cis Coordination of Two Guanines to Copper(II) by d(CGCGCG)2.
Authors: Rohner, M. / Medina-Molner, A. / Spingler, B.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Jan 10, 2024Group: 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
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
C: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
E: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
G: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
H: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,41925
Polymers14,4828
Non-polymers93717
Water1,02757
1
A: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7595
Polymers3,6202
Non-polymers1393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0468
Polymers3,6202
Non-polymers4256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
F: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7595
Polymers3,6202
Non-polymers1393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
H: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8547
Polymers3,6202
Non-polymers2335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.340, 35.253, 47.643
Angle α, β, γ (deg.)90.00, 98.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 1 types, 8 molecules ABCDEFGH

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


Mass: 1810.205 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 6 types, 74 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: MES, calcium lactate, dioxane,

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Data collection

DiffractionMean temperature: 183 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: STOE / Detector: IMAGE PLATE / Date: Oct 27, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.151→24.8696 Å / Num. obs: 5823 / % possible obs: 99.9 % / Observed criterion σ(F): 4 / Redundancy: 1.78 % / Rmerge(I) obs: 0.0612 / Net I/σ(I): 6.31
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 1.55 % / Rmerge(I) obs: 0.2463 / Mean I/σ(I) obs: 0.9 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1834)refinement
X-Areadata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XQY

4xqy
PDB Unreleased entry


Resolution: 2.151→24.8696 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 35.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2997 1100 10.19 %Random selection
Rwork0.2306 ---
obs0.2375 10790 95.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→24.8696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 960 22 57 1039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081080
X-RAY DIFFRACTIONf_angle_d1.081654
X-RAY DIFFRACTIONf_dihedral_angle_d31.176452
X-RAY DIFFRACTIONf_chiral_restr0.052185
X-RAY DIFFRACTIONf_plane_restr0.00648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1515-2.24930.32961360.2731183X-RAY DIFFRACTION94
2.2493-2.36780.37061380.29391222X-RAY DIFFRACTION95
2.3678-2.51610.3691360.28661231X-RAY DIFFRACTION95
2.5161-2.71010.35181310.26651201X-RAY DIFFRACTION96
2.7101-2.98240.37771390.25531226X-RAY DIFFRACTION96
2.9824-3.4130.32261390.23111199X-RAY DIFFRACTION95
3.413-4.29650.2631400.1831201X-RAY DIFFRACTION96
4.2965-24.86960.22191410.20281227X-RAY DIFFRACTION97

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