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- PDB-5gun: Crystal structure of d(GTGGAATGGAAC) -

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Basic information

Entry
Database: PDB / ID: 5gun
TitleCrystal structure of d(GTGGAATGGAAC)
ComponentsDNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
KeywordsDNA / (GGA) motif / DNA expansion in SCA31 patient
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.588 Å
AuthorsSatange, R.B. / Kao, Y.F. / Hou, M.H.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion
Authors: Huang, T.Y. / Chang, C.K. / Kao, Y.F. / Chin, C.H. / Ni, C.W. / Hsu, H.Y. / Hu, N.J. / Hsieh, L.C. / Chou, S.H. / Lee, I.R. / Hou, M.H.
History
DepositionAug 29, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 30, 2017ID: 4RZN
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Mar 20, 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
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.ptnr2_symmetry / _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_conn.ptnr2_symmetry

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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*AP*AP*TP*GP*GP*AP*AP*C)-3')
B: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
C: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
D: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
E: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
F: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,98014
Polymers22,5096
Non-polymers4718
Water25214
1
A: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
B: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6805
Polymers7,5032
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
D: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6214
Polymers7,5032
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
F: DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6805
Polymers7,5032
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.993, 61.993, 208.727
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 3751.466 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50mM sodium cacodylate, 10mM magnesium chloride, 5mM cobalt(II) chloride, 1mM spermine, 8% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.8563, 0.9189, 0.9195
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2011
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.85631
20.91891
30.91951
ReflectionResolution: 2.58→50 Å / Num. obs: 7937 / % possible obs: 98 % / Redundancy: 33 % / Net I/σ(I): 10.3
Reflection shellResolution: 2.58→2.67 Å / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.588→37.419 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2875 365 4.62 %
Rwork0.2429 --
obs0.2449 7894 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.588→37.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1500 8 14 1522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041692
X-RAY DIFFRACTIONf_angle_d0.5192610
X-RAY DIFFRACTIONf_dihedral_angle_d33.131696
X-RAY DIFFRACTIONf_chiral_restr0.025282
X-RAY DIFFRACTIONf_plane_restr0.00272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5878-2.96210.34041100.31032339X-RAY DIFFRACTION95
2.9621-3.73140.28661360.21532484X-RAY DIFFRACTION99
3.7314-37.4230.27221190.24382706X-RAY DIFFRACTION99
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)
11.6428-0.87760.83510.6922-0.35710.5190.03120.82470.5362-0.20790.28290.267-0.2093-0.1493-0.26070.43090.1473-0.11870.77740.15320.77120.8633-12.9574-0.1204
22.3185-0.77340.84640.2845-0.2970.4829-0.18990.76770.3025-0.32020.30890.8257-0.2727-0.2056-0.04350.18360.1276-0.42510.60030.14271.0201-0.6725-13.59440.4397
31.6020.17830.63290.08030.25751.00280.05820.0840.6141-0.345-0.3613-0.2699-0.29980.1783-0.33120.1873-0.12650.27330.90080.18070.815121.583-7.681810.8155
43.05350.9961-0.11570.81860.14410.09170.2276-0.18430.3548-0.1774-0.7291-0.555-0.2470.6108-0.06180.3356-0.19830.04610.85560.24440.577723.2246-8.408310.711
52.7144-0.31630.26050.2339-0.10830.085-0.32650.18790.09480.17330.1366-0.1804-0.40970.32450.08810.2949-0.0803-0.1041.10670.12820.9812-20.6216-21.799211.4351
62.5331-0.41650.36690.0348-0.05710.0534-0.1855-0.19540.3635-0.1498-0.24230.4248-0.2121-0.15550.04090.223-0.1015-0.22051.1264-0.12251.0714-18.9936-22.487910.4675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'B' and (resid 13 through 24 )B13 - 24
3X-RAY DIFFRACTION3chain 'C' and (resid 25 through 36 )C25 - 36
4X-RAY DIFFRACTION4chain 'D' and (resid 37 through 48 )D37 - 48
5X-RAY DIFFRACTION5chain 'E' and (resid 49 through 60 )E49 - 60
6X-RAY DIFFRACTION6chain 'F' and (resid 61 through 72 )F61 - 72

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