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- PDB-4zkk: The novel double-fold structure of d(GCATGCATGC) -

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Basic information

Entry
Database: PDB / ID: 4zkk
TitleThe novel double-fold structure of d(GCATGCATGC)
ComponentsDNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')
KeywordsDNA / folded / minor-groove tetrad / bi-loop / triplet
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsThirugnanasambandam, A. / Karthik, S. / Mandal, P.K. / Gautham, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences
Authors: Thirugnanasambandam, A. / Karthik, S. / Mandal, P.K. / Gautham, N.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
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 / pdbx_struct_oper_list / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_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*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2224
Polymers3,0451
Non-polymers1773
Water43224
1
A: DNA (5'-D(*GP*CP*AP*TP*GP*CP*AP*TP*GP*C)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,4448
Polymers6,0902
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area1520 Å2
ΔGint-41 kcal/mol
Surface area3190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.640, 34.640, 89.601
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-103-

CO

21A-224-

HOH

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Components

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


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CO / COBALT (II) ION


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


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 51.73 % / Description: hexagonal bipyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 mM DNA, 50 mM sodium cacodylate buffer, 10 mM cobalt chloride and equilibrated against 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.604 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2012 / Details: Bent collimating mirror & toroid
RadiationMonochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.604 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 5358 / % possible obs: 98 % / Redundancy: 32 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 36.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.8 / % possible all: 83.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MxCuBE2data collection
MOSFLM7.0.9data processing
PHENIX1.9_1692phasing
MOSFLM7.0.9data reduction
Aimless0.2.14data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.801→24.927 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 0.31 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 541 10.1 %Random selection
Rwork0.2291 ---
obs0.2309 5358 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→24.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 3 24 229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004226
X-RAY DIFFRACTIONf_angle_d0.557347
X-RAY DIFFRACTIONf_dihedral_angle_d32.25996
X-RAY DIFFRACTIONf_chiral_restr0.02439
X-RAY DIFFRACTIONf_plane_restr0.00210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8006-1.98170.2941240.28091079X-RAY DIFFRACTION87
1.9817-2.26830.32831380.27661227X-RAY DIFFRACTION98
2.2683-2.85720.2781390.26971254X-RAY DIFFRACTION99
2.8572-24.92920.221400.20151257X-RAY DIFFRACTION100
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)
10.0159-0.04080.01830.1048-0.04950.02380.07840.00050.0068-0.0595-0.09810.05490.1063-0.00310.01290.0044-0.0627-0.08730.55060.0870.19226.011710.5724-0.0368
20.0480.0175-0.00250.0110.01090.01870.0854-0.0473-0.02290.0084-0.0772-0.12280.10720.03620.0661-0.08210.1266-0.09910.89550.05150.244311.102910.25050.9608
30.04750.02030.02360.0827-0.01510.02130.0346-0.1705-0.0299-0.07340.1023-0.1550.0610.16090.02590.13750.06260.00030.4396-0.01380.358512.824612.1571-10.6452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 3 )
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 7 )
3X-RAY DIFFRACTION3chain 'A' and (resid 8 through 10 )

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