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- PDB-101d: REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTR... -

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Basic information

Entry
Database: PDB / ID: 101d
TitleREFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTRON DENSITY MAP INTERPRETATION
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
MethodX-RAY DIFFRACTION / 2.25 Å resolution
AuthorsGoodsell, D.S. / Kopka, M.L. / Dickerson, R.E.
Citation
Journal: Biochemistry / Year: 1995
Title: Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation.
Authors: Goodsell, D.S. / Kopka, M.L. / Dickerson, R.E.
#1: Journal: J.Mol.Biol. / Year: 1985
Title: Binding of an Antitumor Drug to DNA. Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G
Authors: Kopka, M.L. / Yoon, C. / Goodsell, D.S. / Pjura, P. / Dickerson, R.E.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 14, 1994 / Release: Feb 27, 1995
RevisionDateData content typeGroupProviderType
1.0Feb 27, 1995Structure modelrepositoryInitial release
1.1May 22, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9394
Polyers7,4852
Non-polymers4552
Water64936
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)24.270, 39.620, 63.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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


Mass: 3742.288 Da / Num. of mol.: 2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 1 / Formula: C18H26N10O3 / Netropsin
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 / Density percent sol: 38.45 %
Crystal grow
*PLUS
Method: unknown

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefineSigma F: 2
Least-squares processR factor R free: 0.252 / R factor obs: 0.163 / Highest resolution: 2.25 Å / Lowest resolution: 8 Å / Number reflection obs: 2430
Refine B iso
ClassRefine IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refine hist #LASTHighest resolution: 2.25 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 486 / Ligand: 37 / Solvent: 33 / Total: 556
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it4.2826.000
X-RAY DIFFRACTIONn_sugar_angle_it4.9906.000
X-RAY DIFFRACTIONn_phos_bond_it5.6936.000
X-RAY DIFFRACTIONn_phos_angle_it5.2276.000
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0240.030
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0400.040
X-RAY DIFFRACTIONn_phos_bond_d0.0260.040
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0570.050
X-RAY DIFFRACTIONn_plane_restr0.0140.020
X-RAY DIFFRACTIONn_chiral_restr0.1610.150
X-RAY DIFFRACTIONn_singtor_nbd0.0930.100
X-RAY DIFFRACTIONn_multtor_nbd0.0970.100
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refine
*PLUS
Sigma F: 2
Least-squares process
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 8 Å

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