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- PDB-2gpx: 2'-Me-Se and Br Derivitation of A-DNA Octamer G(UMS)G(BRU)ACAC -

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Basic information

Entry
Database: PDB / ID: 2gpx
Title2'-Me-Se and Br Derivitation of A-DNA Octamer G(UMS)G(BRU)ACAC
Components5'-D(*GP*(UMS)P*GP*(BRU)P*AP*CP*AP*C)-3'
KeywordsDNA / 2'-Methylseleno-uridine / Se-DNA / Se-Br-DNA / Selenium Derivatization
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsJiang, J. / Huang, Z.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Selenium derivatization of nucleic acids for crystallography.
Authors: Jiang, J. / Sheng, J. / Carrasco, N. / Huang, Z.
History
DepositionApr 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.pdbx_leaving_atom_flag / _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_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*(UMS)P*GP*(BRU)P*AP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7082
Polymers2,5701
Non-polymers1371
Water55831
1
A: 5'-D(*GP*(UMS)P*GP*(BRU)P*AP*CP*AP*C)-3'
hetero molecules

A: 5'-D(*GP*(UMS)P*GP*(BRU)P*AP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4164
Polymers5,1412
Non-polymers2752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.252, 42.252, 24.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 2570.447 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Solid Phase Synthesis via Phosphoramidite Chemistry
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% v/v MPD 40mM Sodium Cacodylate, 12mM Spermine tetra-HCI, 80 mM sodium Chloride, 20 mM Barium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1, 0.9797, 0.9196, 0.94
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97971
30.91961
40.941
ReflectionResolution: 1.6→18.9 Å / Num. all: 3161 / Num. obs: 3161 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 9 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.5 / Num. unique all: 297 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
CNSphasing
RefinementStarting model: PDB ENTRY 1Z7I, 2DJL

1z7i

2djl


Resolution: 1.6→18.9 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 421128.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD FUNCTION
RfactorNum. reflection% reflectionSelection details
Rfree0.238 289 9.9 %RANDOM
Rwork0.187 ---
all0.195 ---
obs0.187 2909 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.0464 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.6→18.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 162 1 31 194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d30.5
X-RAY DIFFRACTIONc_improper_angle_d2.09
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 44 11.7 %
Rwork0.213 333 -
obs-333 75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4dna-rna_ums.parion.top
X-RAY DIFFRACTION5ums.top

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