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- PDB-2fil: Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-faT-A... -

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Basic information

Entry
Database: PDB / ID: 2fil
TitleCrystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-faT-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and 2'-Fluoroarabino-Thymidine (faT)
Components5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
KeywordsDNA / 2'-Fluoroarabino Acid / Sugar Modifications / A-form DNA
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsEgli, M. / Li, F.
CitationJournal: Biochemistry / Year: 2006
Title: 2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.
Authors: Li, F. / Sarkhel, S. / Wilds, C.J. / Wawrzak, Z. / Prakash, T.P. / Manoharan, M. / Egli, M.
History
DepositionDec 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
C: 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
D: 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,50011
Polymers12,3724
Non-polymers1,1287
Water3,045169
1
A: 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8316
Polymers6,1862
Non-polymers6444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
D: 5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6695
Polymers6,1862
Non-polymers4833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.733, 69.180, 32.831
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a duplex and corresponds to the crystallographic asymmetric unit, hence no symmetry operators are needed

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Components

#1: DNA chain
5'-D(*GP*CP*GP*TP*(A2M)P*(TAF)P*AP*CP*GP*C)-3'


Mass: 3093.022 Da / Num. of mol.: 4
Mutation: 2'-Methylation at A5 and incorperated 2'-fluoroarabino-T at position 6
Source method: obtained synthetically
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Final droplet composition: 1 mM oligonucleotide, 10% MPD, 20 mM sodium cacodylate, pH 5.5, 10 mM cobalt hexamine, 6 mM NaCl and 80 mM KCl., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3cobalt hexamine11
4NaClSodium chloride11
5KCl11
6H2O11
7MPD12
8sodium cacodylate12
9cobalt hexamine12
10NaClSodium chloride12
11KCl12
12H2O12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→30 Å / Num. all: 15695 / Num. obs: 15695 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.1
Reflection shellResolution: 1.69→1.8 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.8 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB entry AD0007/PDB entry 1DPL

1dpl


Resolution: 1.69→30 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.429 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21543 805 5.1 %RANDOM
Rwork0.20341 ---
obs0.20401 15695 95.7 %-
all-15695 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.247 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20.35 Å2
2---3.9 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 819 49 169 1037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021958
X-RAY DIFFRACTIONr_bond_other_d0.0010.02409
X-RAY DIFFRACTIONr_angle_refined_deg2.5931509
X-RAY DIFFRACTIONr_angle_other_deg1.88131010
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_restr0.2260.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02416
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2850.2250
X-RAY DIFFRACTIONr_nbd_other0.3370.2540
X-RAY DIFFRACTIONr_nbtor_refined0.2850.2322
X-RAY DIFFRACTIONr_nbtor_other0.1230.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4540.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1050.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.216
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_it8.05531389
X-RAY DIFFRACTIONr_scangle_it9.3954.51472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 66 -
Rwork0.333 1111 -
obs--96.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2315-0.2436-0.24313.4926-0.46610.79790.07820.0298-0.09970.2197-0.05770.2128-0.15730.0414-0.02050.0401-0.0084-0.00030.0357-0.00810.012322.5661.26759.8383
20.6377-0.338-0.00073.4513-0.06951.1020.01720.08470.08610.1555-0.0262-0.20690.1005-0.03350.0090.0086-0.00410.00140.05270.0116-0.000825.425118.577226.4573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA101 - 1101 - 10
2X-RAY DIFFRACTION1BB201 - 2101 - 10
3X-RAY DIFFRACTION2CC301 - 3101 - 10
4X-RAY DIFFRACTION2DD401 - 4101 - 10

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