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- PDB-4dy8: Interactions of Mn2+ with a non-self-complementary Z-type DNA duplex -

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Basic information

Entry
Database: PDB / ID: 4dy8
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')
  • DNA (5'-D(P*TP*G)-3')
KeywordsDNA / Z-type DNA double helices / Manganese ions
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 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 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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(P*TP*G)-3')
D: DNA (5'-D(P*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8515
Polymers4,7964
Non-polymers551
Water61334
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)3,6743
Polymers3,6192
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-11 kcal/mol
Surface area2300 Å2
MethodPISA
2
C: DNA (5'-D(P*TP*G)-3')
D: DNA (5'-D(P*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)1,1772
Polymers1,1772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-5 kcal/mol
Surface area1070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.213, 35.213, 44.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*TP*G)-3')


Mass: 588.441 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.6587 Å3/Da / Density % sol: 25.8453 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50% methyl pentane diol, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.0

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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: Sep 28, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.947
11-H-K, K, -L20.053
ReflectionResolution: 1.76→30 Å / Num. all: 3216 / Num. obs: 3133 / % possible obs: 97.4 % / Redundancy: 3.86 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.09 / Net I/σ(I): 4.17
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 3.98 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0109refinement
AUTOMARdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→25.15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.748 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 141 4.6 %RANDOM
Rwork0.2254 ---
obs0.22741 2938 98.5 %-
all-2982 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.9076 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.76→25.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 321 1 34 356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021357
X-RAY DIFFRACTIONr_angle_refined_deg2.3413544
X-RAY DIFFRACTIONr_chiral_restr0.110.261
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02170
X-RAY DIFFRACTIONr_scbond_it2.2933357
X-RAY DIFFRACTIONr_scangle_it2.6514.5544
LS refinement shellResolution: 1.763→1.809 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.118 5 -
Rwork0.216 211 -
obs--96.86 %

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