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- PDB-1i3w: ACTINOMYCIN D BINDING TO CGATCGATCG -

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Basic information

Entry
Database: PDB / ID: 1i3w
TitleACTINOMYCIN D BINDING TO CGATCGATCG
Components
  • 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
  • ACTINOMYCIN DDactinomycin
KeywordsDNA/ANTIBIOTIC / ACTINOMYCIN D / ACTINOMYCIN / ANTIBIOTIC / ANTI CANCER / ANTITUMOR / MISMATCH / CHROMOPHORE / DEPSIPEPTIDE / DNA-ANTIBIOTIC COMPLEX
Function / homologyActinomycin D / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsRobinson, H. / Gao, Y.-G. / Yang, X.-L. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.-J.
CitationJournal: Biochemistry / Year: 2001
Title: Crystallographic Analysis of a Novel Complex of Actinomycin D Bound to the DNA Decamer Cgatcgatcg.
Authors: Robinson, H. / Gao, Y.G. / Yang, X. / Sanishvili, R. / Joachimiak, A. / Wang, A.H.
History
DepositionFeb 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2001Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: pdbx_validate_polymer_linkage / software ...pdbx_validate_polymer_linkage / software / struct_conn / struct_ref_seq
Item: _software.name / _struct_conn.pdbx_leaving_atom_flag ..._software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
B: 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
C: 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
D: 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
E: ACTINOMYCIN D
F: ACTINOMYCIN D
G: ACTINOMYCIN D
H: ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)17,4778
Polymers17,4778
Non-polymers00
Water3,387188
1
A: 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
B: 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
E: ACTINOMYCIN D
F: ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)8,7394
Polymers8,7394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
D: 5'-D(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'
G: ACTINOMYCIN D
H: ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)8,7394
Polymers8,7394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.013, 47.013, 160.368
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(*C*GP*AP*TP*CP*GP*AP*(BRU)P*CP*GP)-3'


Mass: 3109.874 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein/peptide
ACTINOMYCIN D / Dactinomycin / DACTINOMYCIN / Dactinomycin


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1259.447 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (natural) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00228, Actinomycin D
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)

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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: 3.49 Å3/Da / Density % sol: 64.74 %
Crystal growpH: 4.5
Details: GLYCINE BUFFER, BARIUM CHLORIDE, SPERMINE, PEG400, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1glycine buffer11
2barium chloride11
3spermine11
4PEG 40011
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.3 mMDNA single strand1drop
21.3 mMActD1drop
340 mMglycine buffer1drop
410 mM1dropBaCl2
53 mMspermine1drop
64 %PEG4001drop
750 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.953
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 26, 1999
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. obs: 19747 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3 / % possible all: 88.3
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 88.3 % / Rmerge(I) obs: 0.533

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→10 Å / Cross valid method: A POSTERIORI / σ(F): 0
Stereochemistry target values: G. PARKINSON, J. VOJTECHOSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN
Details: SHELX-97 HOPE
RfactorNum. reflection% reflectionSelection details
Rfree0.279 980 5 %RANDOM 5%
all0.239 19747 --
obs0.237 -95.2 %-
Solvent computationSolvent model: SHELX-97 SWAT
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms360 770 0 188 1318
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.068
X-RAY DIFFRACTIONs_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.081
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 17034 / σ(I): 2 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.231 / Rfactor Rwork: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.068
X-RAY DIFFRACTIONs_chiral_restr0.039

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