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- PDB-6jkn: Crystal Structure of G-quadruplex Formed by Bromo-substituted Hum... -

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Basic information

Entry
Database: PDB / ID: 6jkn
TitleCrystal Structure of G-quadruplex Formed by Bromo-substituted Human Telomeric DNA
ComponentsDNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*(BGM)P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*(BGM)P*G)-3')
KeywordsDNA / G-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.401 Å
AuthorsGeng, Y. / Cai, Q. / Liu, C. / Zhu, G.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: The crystal structure of an antiparallel chair-type G-quadruplex formed by Bromo-substituted human telomeric DNA.
Authors: Geng, Y. / Liu, C. / Zhou, B. / Cai, Q. / Miao, H. / Shi, X. / Xu, N. / You, Y. / Fung, C.P. / Din, R.U. / Zhu, G.
History
DepositionMar 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,9454
Polymers6,8281
Non-polymers1173
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint11 kcal/mol
Surface area4090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.252, 46.252, 120.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

21A-318-

HOH

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Components

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


Mass: 6828.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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 / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.71 Å3/Da / Density % sol: 54.69 % / Mosaicity: 0.47 ° / Mosaicity esd: 0.006 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 6
Details: 0.1M sodium cacodylate pH 6.0, 80mM KCl, 12mM NaCl, 12mM spermine tetrahydrochloride, 50% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.91904 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91904 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 15673 / % possible obs: 99.3 % / Redundancy: 32.8 % / Biso Wilson estimate: 18.92 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.013 / Rrim(I) all: 0.076 / Χ2: 0.79 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.4217.21.0596770.8690.2321.0890.44191.7
1.42-1.45211.2367510.9030.2541.2650.42896.8
1.45-1.4823.81.1187600.9340.221.1410.42999.5
1.48-1.5128.31.0897470.9680.2011.1090.43899.1
1.51-1.5433.40.8847820.9970.1520.8980.437100
1.54-1.5835.80.5847550.9950.0980.5920.472100
1.58-1.6236.60.4987720.9960.0830.5050.483100
1.62-1.6636.40.3557720.9950.0590.360.517100
1.66-1.7135.80.297670.9970.0490.2940.543100
1.71-1.7632.50.2187750.9980.0390.2210.611100
1.76-1.8336.30.1897790.9990.0320.1920.622100
1.83-1.937.80.1697730.9990.0280.1710.675100
1.9-1.9937.50.1457840.9990.0240.1470.77799.9
1.99-2.0936.70.127870.9990.0210.1220.884100
2.09-2.2233.90.0958050.9990.0170.0961.161100
2.22-2.3935.90.0867810.9990.0150.0871.234100
2.39-2.6337.30.07480610.0130.0751.19100
2.63-3.0235.10.0678240.9990.0120.0681.275100
3.02-3.831.80.0538410.9990.0090.0541.24599.8
3.8-5029.80.0539350.9970.010.0531.29999.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
PHENIX1.12_2829phasing
RefinementMethod to determine structure: SAD / Resolution: 1.401→37.996 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.1842 1383 4.96 %
Rwork0.159 --
obs0.1602 15571 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.91 Å2 / Biso mean: 30.9781 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: final / Resolution: 1.401→37.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 446 3 119 568
Biso mean--20.19 41.17 -
Num. residues----21
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009502
X-RAY DIFFRACTIONf_angle_d1.854779
X-RAY DIFFRACTIONf_chiral_restr0.06781
X-RAY DIFFRACTIONf_plane_restr0.01621
X-RAY DIFFRACTIONf_dihedral_angle_d32.01208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4011-1.45120.34041400.32382426256691
1.4512-1.50930.29061460.27222636278299
1.5093-1.5780.20641090.20692695280499
1.578-1.66120.19021230.158627002823100
1.6612-1.76530.17971500.146626702820100
1.7653-1.90160.21891510.15326672818100
1.9016-2.09290.25341250.17326982823100
2.0929-2.39570.18971690.163126452814100
2.3957-3.01820.16451460.158826762822100
3.0182-38.01030.15231240.138727102834100

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