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- PDB-6fq2: Structure of minimal sequence for left -handed G-quadruplex formation -

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Basic information

Entry
Database: PDB / ID: 6fq2
TitleStructure of minimal sequence for left -handed G-quadruplex formation
ComponentsDNA (5'-D(*GP*TP*GP*GP*TP*GP*GP*TP*GP*GP*TP*G)-3')
KeywordsDNA / G-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsSchmitt, E. / Mechulam, Y. / Phan, A.T. / Heddi, B. / Bakalar, B.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2019
Title: A Minimal Sequence for Left-Handed G-Quadruplex Formation.
Authors: Bakalar, B. / Heddi, B. / Schmitt, E. / Mechulam, Y. / Phan, A.T.
History
DepositionFeb 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 17, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*TP*GP*GP*TP*GP*GP*TP*GP*GP*TP*G)-3')
B: DNA (5'-D(*GP*TP*GP*GP*TP*GP*GP*TP*GP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7285
Polymers7,6112
Non-polymers1173
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint15 kcal/mol
Surface area3170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.557, 30.557, 53.662
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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


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


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / 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: 1.9 Å3/Da / Density % sol: 35.28 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 55%MPD, 12mM Spermine, 80mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.31→26.46 Å / Num. obs: 2411 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.84 % / CC1/2: 1 / Rsym value: 0.031 / Net I/σ(I): 16.4
Reflection shellResolution: 2.31→2.44 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 379 / CC1/2: 0.93 / Rsym value: 0.23 / % possible all: 96.9

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U5M

4u5m


Resolution: 2.31→26.46 Å / Cross valid method: FREE R-VALUE / Phase error: 27.42
RfactorNum. reflection% reflection
Rfree0.2267 125 5.2 %
Rwork0.1959 --
obs0.1996 2405 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.31→26.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 3 12 521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004568
X-RAY DIFFRACTIONf_angle_d0.697880
X-RAY DIFFRACTIONf_dihedral_angle_d40.336232
X-RAY DIFFRACTIONf_chiral_restr0.03894
X-RAY DIFFRACTIONf_plane_restr0.00224
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)
15.68441.42350.73728.1831-0.07527.11160.1144-0.2899-0.04150.1887-0.1429-0.05910.1614-0.0615-0.0920.4877-0.01760.01630.38210.00780.075515.33610.16673.8713
24.69550.2064-0.22585.2126-0.67697.6941-0.05070.8220.0524-1.17380.4420.02330.09970.1834-0.12620.5459-0.06340.0070.45340.00510.1915.48110.0845-4.2984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 12 )

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