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- PDB-4pwm: Crystal structure of Dickerson Drew Dodecamer with 5-carboxycytosine -

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Basic information

Entry
Database: PDB / ID: 4pwm
TitleCrystal structure of Dickerson Drew Dodecamer with 5-carboxycytosine
Components5'-[CGCGAATT(5CC)GCG]-3'
KeywordsDNA / DNA crystal structure / Dickerson Drew Dodecamer / 5-carboxycytidine / 5-carboxycytosine
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSzulik, M.W. / Pallan, P. / Banerjee, S. / Voehler, M. / Egli, M. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2015
Title: Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.
Authors: Szulik, M.W. / Pallan, P.S. / Nocek, B. / Voehler, M. / Banerjee, S. / Brooks, S. / Joachimiak, A. / Egli, M. / Eichman, B.F. / Stone, M.P.
History
DepositionMar 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 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 / struct_conn
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_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-[CGCGAATT(5CC)GCG]-3'
B: 5'-[CGCGAATT(5CC)GCG]-3'


Theoretical massNumber of molelcules
Total (without water)7,4152
Polymers7,4152
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-3 kcal/mol
Surface area4560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.250, 41.340, 66.410
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 5'-[CGCGAATT(5CC)GCG]-3'


Mass: 3707.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized oligonucleotides
#2: Water ChemComp-HOH / water / 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

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40 mM Na Cacodylate, 12 mM Spermine Tetrahydrochloride, 80 mM SrCl2, 10% MPD , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2013
RadiationMonochromator: rotary beam shutters / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→26 Å / Num. all: 5242 / Num. obs: 5113 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.26
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.8 / Num. unique all: 385 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 436D

436d


Resolution: 1.95→25.89 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.712 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26721 409 8 %RANDOM
Rwork0.22129 ---
obs0.22492 4704 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.709 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 492 0 12 504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.012555
X-RAY DIFFRACTIONr_bond_other_d0.0020.02266
X-RAY DIFFRACTIONr_angle_refined_deg2.2091.307855
X-RAY DIFFRACTIONr_angle_other_deg3.7173632
X-RAY DIFFRACTIONr_chiral_restr0.1640.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02290
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02112
X-RAY DIFFRACTIONr_scbond_it5.3484.691555
X-RAY DIFFRACTIONr_scbond_other5.3464.692554
X-RAY DIFFRACTIONr_scangle_other7.3057.043856
X-RAY DIFFRACTIONr_long_range_B_refined8.22942.681777
X-RAY DIFFRACTIONr_long_range_B_other8.21842.68777
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 30 -
Rwork0.331 352 -
obs--99.48 %

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