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- PDB-4hig: Ultrahigh-resolution crystal structure of Z-DNA in complex with M... -

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Basic information

Entry
Database: PDB / ID: 4hig
TitleUltrahigh-resolution crystal structure of Z-DNA in complex with Mn2+ ion.
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / self-complementary DNA / Z-DNA
Function / homology: / SPERMINE (FULLY PROTONATED FORM) / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.75 Å
AuthorsDrozdzal, P. / Gilski, M. / Kierzek, R. / Lomozik, L. / Jaskolski, M.
Citation
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.
#1: 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.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy.
Authors: Dauter, Z. / Adamiak, D.A.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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

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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8824
Polymers3,6202
Non-polymers2612
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-13 kcal/mol
Surface area2620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.732, 31.436, 43.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SPK / SPERMINE (FULLY PROTONATED FORM)


Mass: 206.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H30N4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.59 Å3/Da / Density % sol: 22.7 %
Crystal growTemperature: 292 K / pH: 6
Details: 1.5 MM DNA WATER SOLUTION MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, HANGING DROP METHOD, ...Details: 1.5 MM DNA WATER SOLUTION MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL, 12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, HANGING DROP METHOD, TEMPERATURE 292K. FOR MN2+ SOAKING, A CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM MNCL2 FOR ONE WEEK.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X1210.801
SYNCHROTRONBESSY 14.220.9184
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDDec 4, 2009
RAYONIX MX-2252CCDMar 16, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.8011
20.91841
ReflectionResolution: 0.75→25.57 Å / Num. obs: 47730 / % possible obs: 79.9 % / Observed criterion σ(I): -3 / Redundancy: 3.28 % / Biso Wilson estimate: 4.756 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.28
Reflection shellResolution: 0.75→0.77 Å / Redundancy: 1.15 % / Rmerge(I) obs: 0.038 / Mean I/σ(I) obs: 11.39 / % possible all: 10.6

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I0T

1i0t


Resolution: 0.75→25.57 Å / Num. parameters: 3409 / Num. restraintsaints: 1139 / Cross valid method: FREE R
Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ADPS. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.1295 TO 0.0903. HYDROGEN ATOMS WERE ADDED AT RIDING ...Details: THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ADPS. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.1295 TO 0.0903. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL MATRIX LEAST-SQUARES PROCEDURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.081 1009 2.11 %RANDOM
all0.071 47730 --
obs0.071 -79.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.(1975) 91, 201.
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 164 / Occupancy sum non hydrogen: 332.97
Refinement stepCycle: LAST / Resolution: 0.75→25.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 15 92 347
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.028
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.069

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