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- PDB-4dwy: Interactions of Mn2+ with a non-self-complementary Z-type DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4dwy
TitleInteractions of Mn2+ with a non-self-complementary Z-type DNA duplex
Components
  • DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')
KeywordsDNA / Z-type DNA double helices
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsMandal, P.K. / Venkadesh, S. / Gautham, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Interactions of Mn(2+) with a non-self-complementary Z-type DNA duplex
Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N.
History
DepositionFeb 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Dec 4, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn / reflns / Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value
Revision 1.3Mar 20, 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_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.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.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_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*AP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')
C: DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3496
Polymers7,2394
Non-polymers1102
Water1,00956
1
A: DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7294
Polymers3,6192
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-10 kcal/mol
Surface area2350 Å2
MethodPISA
2
C: DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6192
Polymers3,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-8 kcal/mol
Surface area2400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.484, 31.128, 31.675
Angle α, β, γ (deg.)90.00, 103.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 1794.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')


Mass: 1825.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.6225 Å3/Da / Density % sol: 24.1913 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM DNA, 50mM sodium cacodylate trihydrate buffer (pH 7.0), 10mM MnCl2, 1mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→15 Å / Num. all: 6048 / Num. obs: 6021 / % possible obs: 97.6 % / Redundancy: 4.43 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.0486 / Rsym value: 0.045 / Net I/σ(I): 8.4
Reflection shellResolution: 1.61→1.66 Å / Redundancy: 4.35 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.2 / Num. unique all: 505 / Rsym value: 0.207 / % possible all: 81.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0109refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→14.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.852 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26689 280 4.7 %RANDOM
Rwork0.19973 ---
obs0.20286 5741 97.55 %-
all-5885 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.3255 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.03 Å2
2--0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.61→14.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 2 56 538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021548
X-RAY DIFFRACTIONr_angle_refined_deg2.8873844
X-RAY DIFFRACTIONr_chiral_restr0.1620.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02252
X-RAY DIFFRACTIONr_scbond_it2.9323548
X-RAY DIFFRACTIONr_scangle_it3.8014.5841
LS refinement shellResolution: 1.606→1.648 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 18 -
Rwork0.349 326 -
obs--74.3 %

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