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- PDB-4hqi: Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-de... -

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Basic information

Entry
Database: PDB / ID: 4hqi
TitleStructure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex
ComponentsShort modified nucleic acids
KeywordsDNA / B-form DNA / O6-Benzyl-2'-deoxyguanosine / dPer / Perimidinone-Derived Nucleoside / Dickerson-Drew Dodecamer
Function / homologySPERMINE / STRONTIUM ION / DNA / DNA (> 10)
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKowal, E.A. / Lad, R. / Pallan, P.S. / Muffly, E. / Wawrzak, Z. / Egli, M. / Sturla, S.J. / Stone, M.P.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.
Authors: Kowal, E.A. / Lad, R.R. / Pallan, P.S. / Dhummakupt, E. / Wawrzak, Z. / Egli, M. / Sturla, S.J. / Stone, M.P.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Feb 28, 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_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_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_conn_type.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

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Assembly

Deposited unit
A: Short modified nucleic acids
B: Short modified nucleic acids
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9434
Polymers7,6532
Non-polymers2902
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-24 kcal/mol
Surface area4860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.384, 36.774, 77.653
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 Short modified nucleic acids


Mass: 3826.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized modified oligonucleotides / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4650.02
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop720 mM sodium cacodylate (pH 7.0), 6 mM spermine tetra-HCl, 20 mM LiCl, 40 mM SrCl2 and 5% v/v 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop720 mM sodium cacodylate (pH 7.0), 6 mM spermine tetra-HCl, 40 mM KCl, 10 mM BaCl2 and 5% v/v 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D11.60499
SYNCHROTRONAPS 21-ID-G20.97857
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDJul 17, 2009Si(111)
MARMOSAIC 300 mm CCD2CCDJul 18, 2008C(111)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2C(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.604991
20.978571
ReflectionResolution: 1.7→30 Å / Num. all: 8811 / Num. obs: 8236 / % possible obs: 93.4 % / Observed criterion σ(I): 5 / Redundancy: 6.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 52.33
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 5.65 / Num. unique all: 524

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→20.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.224 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29823 734 8.9 %RANDOM
Rwork0.25885 ---
obs0.26227 7486 93.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.14 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å2-0 Å2-0 Å2
2--1.38 Å20 Å2
3----4.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 481 15 49 545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.013554
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.578833
X-RAY DIFFRACTIONr_chiral_restr0.1250.266
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02260
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 36 -
Rwork0.336 338 -
obs--57.01 %

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