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- PDB-4r45: Racemic crystal structure of a bimolecular DNA G-quadruplex (P-1) -

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Basic information

Entry
Database: PDB / ID: 4r45
TitleRacemic crystal structure of a bimolecular DNA G-quadruplex (P-1)
Components5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
KeywordsDNA / racemic DNA / racemates
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Racemic DNA crystallography.
Authors: Mandal, P.K. / Collie, G.W. / Kauffmann, B. / Huc, I.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 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 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
B: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8067
Polymers7,6112
Non-polymers1955
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.646, 28.300, 45.719
Angle α, β, γ (deg.)104.50, 94.19, 113.42
Int Tables number2
Space group name H-MP-1

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Components

#1: DNA chain 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'


Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Bimolecular G-Quadruplex / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 1 mM DNA, 50 mM potassium cacodylate, 40 mM potassium chloride, 50 mM magnesium chloride hexahydrate, 2.5 mM spermine, 5% v/v MPD, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 23, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25.02 Å / Num. all: 9497 / Num. obs: 9011 / % possible obs: 94.89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 49.29 Å2 / Rmerge(I) obs: 0.0628 / Net I/σ(I): 7.81
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.1227 / Mean I/σ(I) obs: 2.66 / Num. unique all: 909 / % possible all: 95.66

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.8.0049refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HBN

2hbn


Resolution: 1.9→25.02 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.861 / SU B: 4.668 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34003 412 4.6 %RANDOM
Rwork0.28562 ---
obs0.28797 8599 94.75 %-
all-9075 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.068 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.02 Å20.06 Å2
2--0 Å20.03 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 5 143 654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.011568
X-RAY DIFFRACTIONr_bond_other_d0.0030.02274
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.136880
X-RAY DIFFRACTIONr_angle_other_deg1.6523650
X-RAY DIFFRACTIONr_chiral_restr0.0750.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02300
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02108
X-RAY DIFFRACTIONr_scbond_it0.6190.861568
X-RAY DIFFRACTIONr_scbond_other0.6190.861567
X-RAY DIFFRACTIONr_scangle_other1.021.292881
X-RAY DIFFRACTIONr_long_range_B_refined4.9919.5851070
X-RAY DIFFRACTIONr_long_range_B_other4.3488.642993
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 28 -
Rwork0.337 636 -
obs--95.68 %
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)
11.26070.15630.12431.19240.1382.44260.0315-0.09120.0224-0.0123-0.0071-0.1672-0.0081-0.093-0.02440.0013-0.00080.00310.0154-0.00120.02586.0078-1.658413.9348
21.83190.28240.12280.62360.16162.19790.0820.02380.0328-0.09720.0096-0.15080.1138-0.1022-0.09160.0371-0.00320.02440.0085-0.00110.04635.3067-5.66668.1335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1001 - 1012
2X-RAY DIFFRACTION2B2001 - 2012

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