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- PDB-1kgk: Direct Observation of a Cytosine Analog that Forms Five Hydrogen ... -

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Basic information

Entry
Database: PDB / ID: 1kgk
TitleDirect Observation of a Cytosine Analog that Forms Five Hydrogen Bonds to Guanosine; Guanyl G-Clamp
Components5'-D(*GP*(GCK)P*GP*TP*AP*TP*AP*CP*GP*C)-3'
KeywordsDNA / A-form Double Helix / cytosine analogue
Function / homologyMETHOXY-ETHOXYL / SPERMINE (FULLY PROTONATED FORM) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsWilds, C.J. / Maier, M.A. / Tereshko, V. / Manoharan, M. / Egli, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2002
Title: Direct Observation of a Cytosine Analogue that Forms Five Hydrogen Bonds to Guanosine: Guanidino G-Clamp
Authors: Wilds, C.J. / Maier, M.A. / Tereshko, V. / Manoharan, M. / Egli, M.
History
DepositionNov 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: 5'-D(*GP*(GCK)P*GP*TP*AP*TP*AP*CP*GP*C)-3'
B: 5'-D(*GP*(GCK)P*GP*TP*AP*TP*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8315
Polymers6,4742
Non-polymers3573
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.520, 43.020, 46.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3237.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid phase chemical synthesis.
#2: Chemical ChemComp-MOE / METHOXY-ETHOXYL


Mass: 75.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O2
#3: Chemical ChemComp-SPK / SPERMINE (FULLY PROTONATED FORM) / Spermine


Mass: 206.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H30N4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.84 Å3/Da / Density % sol: 33.07 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6
Details: 1.2 mM DNA, 5% MPD, 20 mM Sodium Cacodylate, 40 mM sodium chloride, 6 mM potassium chloride, 10 mM magnesium chloride; equilibrated against 35% MPD, pH 6.0, Hanging Drop, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Sodium Cacodylate11
3NaClSodium chloride11
4KCl11
5MgCl211
6MPD11
7NaClSodium chloride12
8KCl12
9MgCl212
10MPD12
11Sodium Cacodylate12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.2 mMDNA1drop
25 %MPD1drop
320 mMsodium cacodylate1droppH6.0
46 mMspermine 4HCl1drop
540 mM1dropNaCl
66 mM1dropKCl
710 mM1dropMgCl2
835 %(v/v)MPD1reservoir
91
101
111

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 29, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1→10 Å / Num. all: 27320 / Num. obs: 27320 / % possible obs: 99.6 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 1→1.1 Å / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→10 Å / Num. parameters: 5528 / Num. restraintsaints: 26595
RfactorNum. reflection% reflection
all0.128 27320 -
obs-27320 99.6 %
Refine analyzeOccupancy sum hydrogen: 283.5 / Occupancy sum non hydrogen: 608
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 686 68 155 909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_from_restr_planes0.222
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.055
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1 Å / Lowest resolution: 1.1 Å / Num. reflection obs: 6666 / Rfactor all: 0.13

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