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- PDB-3fq5: Crystal Structure of d(CACGCG).d(CGCGTG) with 10mM MnCl2 -

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Basic information

Entry
Database: PDB / ID: 3fq5
TitleCrystal Structure of d(CACGCG).d(CGCGTG) with 10mM MnCl2
Components
  • 5'-D(*CP*AP*CP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*GP*TP*G)-3'
KeywordsDNA / Double helix
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVenkadesh, S. / Kannan, R. / Mandal, P.K. / Gautham, N.
CitationJournal: To be Published
Title: Crystal Structure of d(CACGCG).d(CGCGTG) with 10mM MnCl2
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionJan 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 28, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 5'-D(*CP*AP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*TP*G)-3'
C: 5'-D(*CP*AP*CP*GP*CP*G)-3'
D: 5'-D(*CP*GP*CP*GP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3496
Polymers7,2394
Non-polymers1102
Water21612
1
A: 5'-D(*CP*AP*CP*GP*CP*G)-3'
B: 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 area650 Å2
ΔGint-6 kcal/mol
Surface area2320 Å2
MethodPISA
2
C: 5'-D(*CP*AP*CP*GP*CP*G)-3'
D: 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 area610 Å2
ΔGint-5 kcal/mol
Surface area2410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.612, 31.257, 31.962
Angle α, β, γ (deg.)90.00, 103.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 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 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.: 12 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.99
Details: 50mM Sodium Cacodylate buffer, 10mM MnCl2, 1mM Spermine, 50% MPD, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Cacodylate11
2MnCl211
3Spermine11
4MPD11
5Sodium Cacodylate12
6MnCl212
7MPD12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2007
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. all: 1241 / Num. obs: 1179 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 2.88 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 8
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 3.3 / Num. unique all: 72 / Rsym value: 0.1149 / % possible all: 94.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→14.71 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.551 / SU ML: 0.248 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20162 61 5.2 %RANDOM
Rwork0.16485 ---
obs0.16692 1108 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.01 Å2
2---0.15 Å20 Å2
3----0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.327 Å
Refinement stepCycle: LAST / Resolution: 2.8→14.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 2 12 494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.021536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.4563820
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1520.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02252
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2196
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3410.2279
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0210.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it4.1223793
X-RAY DIFFRACTIONr_scangle_it4.8964.5820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 1 -
Rwork0.295 77 -
obs-72 95.12 %

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