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- PDB-5ihd: Calcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), ... -

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Basic information

Entry
Database: PDB / ID: 5ihd
TitleCalcium(II) and copper(II) bound to the Z-DNA form of d(CGCGCG), complexed by L-lactate and succinate
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / copper(II)
Function / homology(2S)-2-HYDROXYPROPANOIC ACID / COPPER (II) ION / SUCCINIC ACID / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsRohner, M. / Medina-Molner, A. / Spingler, B.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200220-100752 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
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionJun 29, 2016ID: 4XQY
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,87313
Polymers7,2414
Non-polymers6339
Water2,396133
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)4,0318
Polymers3,6202
Non-polymers4116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-15 kcal/mol
Surface area2550 Å2
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)3,8425
Polymers3,6202
Non-polymers2223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-15 kcal/mol
Surface area2440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.487, 35.576, 31.044
Angle α, β, γ (deg.)90.00, 107.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 1 types, 4 molecules ABCD

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


Mass: 1810.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 142 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / 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-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 6
Details: 1.2 mM d(CG)3, 1.2 mM di copper complex, 0.25 M MES pH 6, 25 mM Ca(lactate)2, 2.5% EtOAc

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Data collection

DiffractionMean temperature: 183 K
Diffraction sourceSource: SEALED TUBE / Type: Long fine focus / Wavelength: 1.54 Å
DetectorType: STOE / Detector: IMAGE PLATE / Date: Nov 7, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.57→26.215 Å / Num. obs: 7934 / % possible obs: 97.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.51
Reflection shellResolution: 1.57→1.7 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.1736 / Mean I/σ(I) obs: 3.77 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIXdev_1834refinement
X-Areadata reduction
XSCALEdata scaling
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DCG

2dcg


Resolution: 1.57→26.215 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.2
RfactorNum. reflection% reflection
Rfree0.19 408 5.14 %
Rwork0.1605 --
obs0.162 7934 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.57→26.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 26 133 639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007570
X-RAY DIFFRACTIONf_angle_d1.048873
X-RAY DIFFRACTIONf_dihedral_angle_d29.428244
X-RAY DIFFRACTIONf_chiral_restr0.05498
X-RAY DIFFRACTIONf_plane_restr0.00728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5701-1.79720.20771250.17362391X-RAY DIFFRACTION94
1.7972-2.26410.21991370.17032564X-RAY DIFFRACTION100
2.2641-26.21850.17181460.15182571X-RAY DIFFRACTION100

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