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- PDB-4r15: High-resolution crystal structure of Z-DNA in complex with Cr3+ c... -

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Basic information

Entry
Database: PDB / ID: 4r15
TitleHigh-resolution crystal structure of Z-DNA in complex with Cr3+ cations
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / SELF-COMPLEMENTARY DNA / Z-DNA
Function / homologyCHROMIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsDrozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2015
Title: High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations.
Authors: Drozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions.
Authors: Drozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution.
Authors: Luo, Z. / Dauter, M. / Dauter, Z.
#3: Journal: Nucleic Acids Res. / Year: 2011
Title: High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.
Authors: Brzezinski, K. / Brzuszkiewicz, A. / Dauter, M. / Kubicki, M. / Jaskolski, M. / Dauter, Z.
History
DepositionAug 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 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_asym_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.ptnr3_auth_asym_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.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.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_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: 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)3,7765
Polymers3,6202
Non-polymers1563
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-28 kcal/mol
Surface area2330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)18.140, 30.440, 42.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsSelf-complementary dimer of chains A and B

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Components

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


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHETIC CONSTRUCT
#2: Chemical ChemComp-CR / CHROMIUM ION


Mass: 51.996 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.66 Å3/Da / Density % sol: 24.88 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: A 1.5 MM WATER SOLUTION OF DNA MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. FOR CR3+ SOAKING, THE CRYSTAL WAS PLACED FOR ...Details: A 1.5 MM WATER SOLUTION OF DNA MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE*4HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. FOR CR3+ SOAKING, THE CRYSTAL WAS PLACED FOR SEVERAL DAYS IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM [CR(H2O)6]CL3, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 30, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 0.97→24.83 Å / Num. all: 26535 / Num. obs: 26535 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.53 % / Biso Wilson estimate: 13.586 Å2 / Rmerge(I) obs: 0.016 / Net I/σ(I): 24.85
Reflection shellResolution: 0.973→1 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.05 / % possible all: 93.2

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HIF

4hif


Resolution: 0.97→24.83 Å / Num. parameters: 3347 / Num. restraintsaints: 6729 / Cross valid method: FREE R
StereochEM target val spec case: PHOSPHATE AND GLYCOSIDIC ANGLES ACCORDING TO PDB MODEL 3P4J
Stereochemistry target values: CLOWNEY, GELBIN & PARKINSON
Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ATOMIC DISPLACEMENT PARAMETERS WERE USED. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.2585 TO 0.1976. ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ATOMIC DISPLACEMENT PARAMETERS WERE USED. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.2585 TO 0.1976. HYDROGEN ATOMS WERE ADDED AT RIDING POSITION THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL-MATRIX LEAST-SQUARES PROCEDURE AND ALL REFLECTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 1858 7 %RANDOM
Rwork0.1438 ---
all0.1447 26535 --
obs0.1438 -98.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.(1975) 91, 201
Refine analyzeNum. disordered residues: 13 / Occupancy sum hydrogen: 136 / Occupancy sum non hydrogen: 280.78
Refinement stepCycle: LAST / Resolution: 0.97→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 3 67 310
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0378
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.029
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.009
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0.096

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