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- PDB-4c63: ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5- METH... -

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Basic information

Entry
Database: PDB / ID: 4c63
TitleULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5- METHYLCYSTOSINE MODIFICATION
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*5CMP*GP*CP*GP)-3'
KeywordsDNA / CYTOSINE MODIFICATION
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsMcdonough, M. / El-Sagheer, A.H. / Brown, T. / Schofield, C.J.
CitationJournal: Chem. Commun. (Camb.) / Year: 2014
Title: Structural insights into how 5-hydroxymethylation influences transcription factor binding.
Authors: Lercher, L. / McDonough, M.A. / El-Sagheer, A.H. / Thalhammer, A. / Kriaucionis, S. / Brown, T. / Schofield, C.J.
History
DepositionSep 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3May 7, 2014Group: Structure summary
Revision 1.4Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_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*GP*CP*GP*AP*AP*TP*TP*5CMP*GP*CP*GP)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*5CMP*GP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3793
Polymers7,3552
Non-polymers241
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint0.6 kcal/mol
Surface area4320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.456, 40.060, 65.414
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'-D(*CP*GP*CP*GP*AP*AP*TP*TP*5CMP*GP*CP*GP)-3'


Mass: 3677.419 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: 5-METHYL CYTOSINE AT POSITION C9 STRAND A AND C21 STRAND B, DICKERSON-DREW SEQUENCE DODECAMER
Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.02 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7.5
Details: 40% MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 6, 2011 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.3→25.34 Å / Num. obs: 16355 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 19.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2.3 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BNA

1bna


Resolution: 1.32→25.335 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 18.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1848 1503 10 %
Rwork0.1497 --
obs0.1534 15039 95.57 %
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.41 Å2 / ksol: 0.506 e/Å3
Displacement parametersBiso mean: 24.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.8962 Å20 Å20 Å2
2---1.8127 Å20 Å2
3----1.0835 Å2
Refinement stepCycle: LAST / Resolution: 1.32→25.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 488 1 94 583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021552
X-RAY DIFFRACTIONf_angle_d2.364855
X-RAY DIFFRACTIONf_dihedral_angle_d31.124224
X-RAY DIFFRACTIONf_chiral_restr0.11392
X-RAY DIFFRACTIONf_plane_restr0.03324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3201-1.36270.28211170.2251086X-RAY DIFFRACTION85
1.3627-1.41140.29551270.19191129X-RAY DIFFRACTION90
1.4114-1.46790.221300.16291186X-RAY DIFFRACTION93
1.4679-1.53470.19491340.13961165X-RAY DIFFRACTION93
1.5347-1.61560.20651380.1131234X-RAY DIFFRACTION97
1.6156-1.71680.15651350.10011249X-RAY DIFFRACTION98
1.7168-1.84930.1681410.10961266X-RAY DIFFRACTION99
1.8493-2.03530.17211440.14191283X-RAY DIFFRACTION99
2.0353-2.32960.20211400.151277X-RAY DIFFRACTION99
2.3296-2.93440.24271460.17311301X-RAY DIFFRACTION99
2.9344-25.340.15541510.15271360X-RAY DIFFRACTION97

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