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- PDB-1qfi: SYNTHESIS AND STRUCTURE OF PROLINE RING MODIFIED ACTINOMYCINS OF ... -

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Basic information

Entry
Database: PDB / ID: 1qfi
TitleSYNTHESIS AND STRUCTURE OF PROLINE RING MODIFIED ACTINOMYCINS OF X TYPE
ComponentsACTINOMYCIN X2
KeywordsANTIBIOTIC / ACTINOMYCIN / ANTICANCER / ANTITUMOR / CHROMOPHORE / DEPSIPEPTIDE
Function / homologyActinomycin X2 / ETHYL ACETATE / METHANOL / :
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodX-RAY DIFFRACTION / DIRECT METHODS / Resolution: 0.91 Å
AuthorsLifferth, A. / Bahner, I. / Lackner, H. / Schaefer, M.
CitationJournal: Z.Naturforsch. / Year: 1999
Title: Synthesis and Structure of Proline Ring Modified Actinomycins of the X-Type
Authors: Lifferth, A. / Bahner, I. / Lackner, H. / Schaefer, M.
History
DepositionApr 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: 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 1.5Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software / Item: _software.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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 / _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: ACTINOMYCIN X2
B: ACTINOMYCIN X2
C: ACTINOMYCIN X2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,59715
Polymers3,8203
Non-polymers77712
Water0
1
A: ACTINOMYCIN X2
hetero molecules


  • defined by author
  • 1.75 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,7467
Polymers1,2731
Non-polymers4736
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACTINOMYCIN X2


Theoretical massNumber of molelcules
Total (without water)1,2731
Polymers1,2731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ACTINOMYCIN X2
hetero molecules


  • defined by author
  • 1.58 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,5787
Polymers1,2731
Non-polymers3046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)15.594, 16.009, 25.322
Angle α, β, γ (deg.)86.23, 85.16, 69.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide ACTINOMYCIN X2 / ACTINOMYCIN V


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1273.431 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: ACTINOMYCIN X2 CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (synth.) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00232, Actinomycin X2
#2: Chemical
ChemComp-EEE / ETHYL ACETATE / Ethyl acetate


Mass: 88.105 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical
ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH4O
Compound detailsACTINOMYCIN X2 IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN X2 IS ...ACTINOMYCIN X2 IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN X2 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: 1.12 Å3/Da / Density % sol: 20.37 %
Crystal growpH: 5 / Details: PH 5.00

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54178
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 0.91→25.15 Å / Num. obs: 15506 / % possible obs: 94.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.047 / Rsym value: 0.015 / Net I/σ(I): 43.4
Reflection shellResolution: 0.91→1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 14.7 / Rsym value: 0.066 / % possible all: 82.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.91→25.15 Å / Num. parameters: 2994 / Num. restraintsaints: 3955 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
all0.065 15506 -
obs--94.2 %
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 307.6 / Occupancy sum non hydrogen: 310.8
Refinement stepCycle: LAST / Resolution: 0.91→25.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms273 0 52 0 325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.027
X-RAY DIFFRACTIONs_from_restr_planes0.124
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.056

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