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- PDB-7ech: Crystal Structure of d(G4C2)2-K in F222 space group -

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Basic information

Entry
Database: PDB / ID: 7ech
TitleCrystal Structure of d(G4C2)2-K in F222 space group
ComponentsDNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
KeywordsDNA / G-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsGeng, Y. / Liu, C. / Cai, Q. / Luo, Z. / Zhu, G.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Crystal structure of parallel G-quadruplex formed by the two-repeat ALS- and FTD-related GGGGCC sequence.
Authors: Geng, Y. / Liu, C. / Cai, Q. / Luo, Z. / Miao, H. / Shi, X. / Xu, N. / Fung, C.P. / Choy, T.T. / Yan, B. / Li, N. / Qian, P. / Zhou, B. / Zhu, G.
History
DepositionMar 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
B: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,54911
Polymers11,2363
Non-polymers3138
Water1086
1
A: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,60720
Polymers14,9824
Non-polymers62616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y+1/2,-z-1/21
crystal symmetry operation11_454-x-1/2,y,-z-1/21
crystal symmetry operation14_455-x-1/2,-y+1/2,z1
Buried area6080 Å2
ΔGint-33 kcal/mol
Surface area6100 Å2
MethodPISA
2
B: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
hetero molecules

B: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,29412
Polymers14,9824
Non-polymers3138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_445-x-1/2,-y-1/2,z1
Buried area5330 Å2
ΔGint-34 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.216, 61.059, 110.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-102-

K

31A-103-

K

41A-104-

K

51B-102-

K

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DC / End label comp-ID: DC / Refine code: 0 / Auth seq-ID: 1 - 12 / Label seq-ID: 1 - 12

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')


Mass: 3745.416 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6.5
Details: 50 mM Sodium Cacodylate trihydrate pH 6.0, 45% MPD, 12 mM spermine tetrahydrochloride, 80 mM KCl and 20 mM MgCl2 with the same reservoir buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 3951 / % possible obs: 97.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.028 / Rrim(I) all: 0.089 / Χ2: 2.078 / Net I/σ(I): 12.5 / Num. measured all: 41272
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.38-2.428.40.4551920.950.1470.480.81891.4
2.42-2.479.10.4851700.9710.1560.5110.86991.4
2.47-2.51100.3551870.9810.1110.3730.95293
2.51-2.5610.50.2931920.9910.090.3071.00793.7
2.56-2.6210.50.2561910.9970.0780.2681.02997.4
2.62-2.6810.80.2341880.9980.0720.2461.049100
2.68-2.7511.30.2642020.9970.080.2770.95499.5
2.75-2.8211.10.2661950.9950.0810.2790.99399
2.82-2.910.30.2621930.9930.0860.2761.76697.5
2.9-312.50.2022060.9960.0610.2121.648100
3-3.1112.20.1511970.9980.0480.1592.03100
3.11-3.2311.80.0951990.9990.0320.1012.36899.5
3.23-3.3811.60.0871930.9980.0320.0932.45699
3.38-3.5511.20.1022020.9990.0350.1082.45699.5
3.55-3.7811.10.1011990.9990.0340.1072.67999
3.78-4.0710.20.0712050.9980.0230.0752.998100
4.07-4.488.60.0712000.9990.0250.0753.9199
4.48-5.1310.10.0582110.9990.0190.0613.71100
5.13-6.469.50.062040.9980.0190.0633.87100
6.46-5080.0512250.9960.0180.0554.06397

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ECG

7ecg


Resolution: 2.38→39.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.605 / SU ML: 0.162 / SU R Cruickshank DPI: 0.5922 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.592 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 217 5.5 %RANDOM
Rwork0.2149 ---
obs0.2169 3734 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.88 Å2 / Biso mean: 72.272 Å2 / Biso min: 30.64 Å2
Baniso -1Baniso -2Baniso -3
1-7.07 Å20 Å2-0 Å2
2---3.1 Å2-0 Å2
3----3.97 Å2
Refinement stepCycle: final / Resolution: 2.38→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 747 8 6 761
Biso mean--50.24 56.21 -
Num. residues----36
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.011861
X-RAY DIFFRACTIONr_bond_other_d0.0030.02410
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.1361328
X-RAY DIFFRACTIONr_angle_other_deg1.5983965
X-RAY DIFFRACTIONr_chiral_restr0.1140.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02479
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02222
Refine LS restraints NCS

Ens-ID: 1 / Number: 940 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.381→2.443 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 20 -
Rwork0.287 250 -
all-270 -
obs--91.22 %

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