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- PDB-7ecf: Crystal Structure of d(G4C2)2-Ba in C2221 space group -

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Basic information

Entry
Database: PDB / ID: 7ecf
TitleCrystal Structure of d(G4C2)2-Ba in C2221 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 / SAD / Resolution: 1.6 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 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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')
D: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
E: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
F: 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)23,43413
Polymers22,4726
Non-polymers9617
Water1,47782
1
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')
hetero molecules

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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,80610
Polymers14,9824
Non-polymers8246
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
2
C: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
hetero molecules

C: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
D: 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)15,5318
Polymers14,9824
Non-polymers5494
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
3
E: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
F: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
hetero molecules

E: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')
F: 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)15,5318
Polymers14,9824
Non-polymers5494
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Unit cell
Length a, b, c (Å)60.841, 110.076, 56.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23E
14B
24C
15B
25D
16B
26E
17C
27E
18C
28F
19E
29F

NCS domain segments:

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

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23EE
14BB
24CC
15BB
25DD
16BB
26EE
17CC
27EE
18CC
28FF
19EE
29FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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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.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Mosaicity: 0.465 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 7
Details: 40 mM Sodium Cacodylate trihydrate pH 7.0, 10% MPD, 12 mM spermine tetrahydrochloride, 80 mM NaCl and 20 mM BaCl2 with the reservoir buffer of 17.5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 25435 / % possible obs: 99.3 % / Redundancy: 12 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.027 / Rrim(I) all: 0.09 / Χ2: 1.906 / Net I/σ(I): 7.9 / Num. measured all: 304529
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.639.90.68611650.9670.2190.7210.55492.8
1.63-1.6610.40.53312510.9830.1660.5590.62497.7
1.66-1.6911.20.53112330.9750.1620.5560.60299.5
1.69-1.72120.44312670.9790.1330.4630.65100
1.72-1.7612.40.44512600.9750.1320.4640.684100
1.76-1.812.20.35512740.9840.1070.3710.744100
1.8-1.8512.20.33512650.9770.0990.3490.79199.7
1.85-1.910.90.2712460.9890.0840.2830.82499.4
1.9-1.9513.10.24612580.9880.0710.2560.89699.8
1.95-2.0213.10.21412830.990.0620.2230.937100
2.02-2.0913.10.17512630.9950.0510.1831.117100
2.09-2.17130.14912840.9950.0430.1561.39799.9
2.17-2.2712.70.13312620.9960.0390.1381.594100
2.27-2.3911.50.11212700.9940.0350.1181.86499.3
2.39-2.5412.70.08512780.9980.0250.0882.02599.8
2.54-2.7413.30.07113000.9980.0210.0742.428100
2.74-3.0112.60.08112910.9980.0240.0843.71199.9
3.01-3.45110.07212870.9960.0230.0764.6399.3
3.45-4.3411.60.0713130.9980.0210.0735.40499.8
4.34-5010.50.07913850.9970.0260.0836.54299.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→38.84 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 3.067 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1713 1288 5.1 %RANDOM
Rwork0.1409 ---
obs0.1426 24134 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 181.51 Å2 / Biso mean: 48.57 Å2 / Biso min: 21.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å2-0 Å2-0 Å2
2---2.71 Å2-0 Å2
3---5.45 Å2
Refinement stepCycle: final / Resolution: 1.6→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1494 7 82 1583
Biso mean--28.73 47.93 -
Num. residues----72
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0111680
X-RAY DIFFRACTIONr_bond_other_d0.0020.02798
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.1342592
X-RAY DIFFRACTIONr_angle_other_deg1.59831878
X-RAY DIFFRACTIONr_chiral_restr0.1060.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02936
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02432
X-RAY DIFFRACTIONr_rigid_bond_restr8.39832476
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A9840.14
12B9840.14
21A9630.1
22C9630.1
31A9710.1
32E9710.1
41B9560.14
42C9560.14
51B9600.13
52D9600.13
61B9590.14
62E9590.14
71C9510.12
72E9510.12
81C9430.16
82F9430.16
91E9440.15
92F9440.15
LS refinement shellResolution: 1.6→1.638 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.221 52 -
Rwork0.235 1639 -
obs--90.57 %

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