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- PDB-1d8g: ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG) -

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Basic information

Entry
Database: PDB / ID: 1d8g
TitleULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)
Components5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*GP*)-3'
KeywordsDNA / B-DNA / ALTERNATE CONFORMATION / ULTRAHIGH RESOLUTION / TRP REPRESSOR / POLYAMIDE
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.74 Å
AuthorsKielkopf, C.L. / Ding, S. / Kuhn, P. / Rees, D.C.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2).
Authors: Kielkopf, C.L. / Ding, S. / Kuhn, P. / Rees, D.C.
History
DepositionOct 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Feb 7, 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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.ptnr1_symmetry / _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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,2055
Polymers3,0451
Non-polymers1604
Water2,144119
1
A: 5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*GP*)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,41110
Polymers6,0902
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)31.735, 25.703, 34.215
Angle α, β, γ (deg.)90.00, 116.90, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-253-

HOH

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Components

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


Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MPD, CALCIUM ACETATE, TRIS(HYDROXYAMINOMETHANE) BUFFER, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1CALCIUM ACETATE,11
2TRIS(HYDROXYAMINOMETHANE) BUFFER11
3MPD11
4MPD12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6 mMduplex DNA1drop
250 mMcalcium acetate1drop
314 %1drop
45 mMTris-HCl1drop
528 %MPD1reservoir
6100 mMcalcium acetate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSSRL BL9-120.98
SYNCHROTRONSSRL BL9-130.78
Detector
TypeIDDetectorDetails
RIGAKU RAXIS IV1IMAGE PLATE
MARRESEARCH2IMAGE PLATEDOUBLE FOCUSSING MIRRORS
MARRESEARCH3IMAGE PLATEDOUBLE FOCUSSING MIRRORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.981
30.781
ReflectionResolution: 0.74→16 Å / Num. all: 29991 / Num. obs: 29991 / % possible obs: 90 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 26.7
Reflection shellResolution: 0.74→0.75 Å / Rmerge(I) obs: 0.239 / % possible all: 71.1
Reflection
*PLUS
Num. measured all: 130259
Reflection shell
*PLUS
% possible obs: 71.1 % / Mean I/σ(I) obs: 6.9

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 0.74→16 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: SADI RESTRAINTS ON BACKBONE
RfactorNum. reflection% reflectionSelection details
Rfree0.131 1783 5.9 %RANDOM
all0.105 29991 --
obs0.105 29991 90 %-
Refinement stepCycle: LAST / Resolution: 0.74→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 4 119 325
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 28208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.028
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.19

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