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- PDB-2h0n: Structure of the fully modified left-handed cyclohexene nucleic a... -

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Entry
Database: PDB / ID: 2h0n
TitleStructure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC
Components5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'
KeywordsDNA / CYCLOHEXENE NUCLEIC ACID / DNA ANALOGUE / LEFT-HANDED / DOUBLE HELIX
Function / homologyDIHYDROGENPHOSPHATE ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsRobeyns, K. / Van Meervelt, L.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC.
Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L.
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all ..._reflns_shell.number_unique_all / _reflns_shell.percent_possible_all / _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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_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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'
B: 5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2084
Polymers5,0142
Non-polymers1942
Water1,11762
1
A: 5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'
hetero molecules

A: 5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2084
Polymers5,0142
Non-polymers1942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
2
B: 5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'
hetero molecules

B: 5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2084
Polymers5,0142
Non-polymers1942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
Unit cell
Length a, b, c (Å)41.455, 41.455, 65.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-10-

HOH

21A-11-

HOH

31B-10-

HOH

41B-11-

HOH

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Components

#1: DNA chain 5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'


Mass: 2506.921 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION / Dihydrogen phosphate


Mass: 96.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O4P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED CACODYLATE BUFFER, LICL, SRCL2, MGCL2, SPERMINE TETRACHLORIDE, AND MPD, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1CACODYLATECacodylic acid11
2LICL11
3SRCL211
4MGCL211
5SPERMINE11
6TETRACHLORIDE11
7MPD11
8H2O11
9CACODYLATECacodylic acid12
10LICL12
11SRCL212
12MGCL212
13MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8126 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 18, 2005
RadiationMonochromator: triangular horizontal-focusing Si III monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 1.53→20 Å / Num. all: 3416 / Num. obs: 3396 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 11.5667 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.8
Reflection shellResolution: 1.53→1.58 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 5.58 / Num. unique all: 333

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Processing

Software
NameVersionClassification
SHELXL-97refinement
MAR345345data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1.60A P 32 1 2 STRUCTURE OF H(GTGTACAC) (NDB CODE HD0001) WAS USED AS MODEL

Resolution: 1.53→20 Å / Num. parameters: 1620 / Num. restraintsaints: 1514 / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0
StereochEM target val spec case: ALL OTHER CHEMICALLY EQUIVALENT BOND DISTANCES AND ANGLES WERE RESTRAINED TO BE SIMILAR BY SAME DISTANCE RESTRAINTS
Stereochemistry target values: Engh & Huber
Details: CHAIN A AND B ARE REFINED AS BEING STATICALLY DISORDERED
RfactorNum. reflection% reflection
Rwork0.1581 --
all0.2004 3396 -
obs0.2004 3396 98.5 %
Displacement parametersBiso mean: 20.21 Å2
Refine analyzeNum. disordered residues: 80 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 201.67
Refinement stepCycle: LAST / Resolution: 1.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 336 8 62 406
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_from_restr_planes0.001
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
LS refinement shellResolution: 1.53→1.58 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.412 --
obs-333 99.7 %

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