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- PDB-4pzq: Crystal Structure of CCG DNA repeats -

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Basic information

Entry
Database: PDB / ID: 4pzq
TitleCrystal Structure of CCG DNA repeats
ComponentsDNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')
KeywordsDNA / i-motif / hemiprotonated CC+ pairs / CCG triplet repeat
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 Å
AuthorsChen, Y.W. / Hou, M.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Structural basis for the identification of an i-motif tetraplex core with a parallel-duplex junction as a structural motif in CCG triplet repeats
Authors: Chen, Y.W. / Jhan, C.R. / Neidle, S. / Hou, M.H.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 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 / struct_site
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_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.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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,4133
Polymers3,2951
Non-polymers1182
Water1,08160
1
A: DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,8266
Polymers6,5902
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Unit cell
Length a, b, c (Å)38.145, 38.145, 54.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-222-

HOH

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Components

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


Mass: 3295.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Humans. / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50MM SODIUM CACODYLATE, 1MM MAGNESIUM CHLORIDE, 5% MPD, 2MM COBALT(II) CHLORIDE, 1MM CHROMOMYCIN A3, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.56418, 1.60467, 1.60553
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2012
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.564181
21.604671
31.605531
ReflectionResolution: 2.24→30 Å / Num. obs: 2159 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.04
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.851 / % possible all: 94.4

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.24→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 136 RANDOM
Rwork0.235 --
all0.2361 3669 -
obs0.235 2004 -
Refinement stepCycle: LAST / Resolution: 2.24→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 218 2 60 280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.073

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