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- PDB-1a7z: CRYSTAL STRUCTURE OF ACTINOMYCIN Z3 -

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Basic information

Entry
Database: PDB / ID: 1a7z
TitleCRYSTAL STRUCTURE OF ACTINOMYCIN Z3
ComponentsACTINOMYCIN Z3
KeywordsANTIBIOTIC / ACTINOMYCIN D / ACTINOMYCIN / ANTICANCER / ANTITUMOR / CHROMOPHORE / DEPSIPEPTIDE
Function / homologyActinomycin Z3 / BENZENE / :
Function and homology information
Biological speciesSTREPTOMYCES FRADIAE (bacteria)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 0.95 Å
AuthorsSchafer, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 1998
Title: Crystal Structures of Actinomycin D and Actinomycin Z3.
Authors: Schafer, M. / Sheldrick, G.M. / Bahner, I. / Lackner, H.
History
DepositionMar 19, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: 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 1.5Mar 7, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status / pdbx_validate_polymer_linkage
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.6Nov 13, 2019Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_id_ASTM / _citation.journal_id_CSD ..._citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
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 Z3
B: ACTINOMYCIN Z3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,21022
Polymers2,6482
Non-polymers1,56220
Water181
1
A: ACTINOMYCIN Z3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,9499
Polymers1,3241
Non-polymers6258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACTINOMYCIN Z3
hetero molecules


  • defined by author
  • 2.26 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2,26113
Polymers1,3241
Non-polymers93712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)14.803, 24.780, 65.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide ACTINOMYCIN Z3


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1323.876 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ACTINOMYCIN Z3 CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (natural) STREPTOMYCES FRADIAE (bacteria) / References: NOR: NOR00237, Actinomycin Z3
#2: Chemical
ChemComp-BNZ / BENZENE / Benzene


Mass: 78.112 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C6H6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTINOMYCIN Z3 IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCIN Z3 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: PH 7
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Common name: benzene

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 22, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.95→32.45 Å / Num. obs: 15653 / % possible obs: 99.5 % / Redundancy: 7.06 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.17
Reflection shellResolution: 0.95→1.05 Å / Redundancy: 4.85 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.93 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 112696 / Rmerge(I) obs: 0.0602

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: AB INITIO / Resolution: 0.95→32.45 Å / Num. parameters: 3024 / Num. restraintsaints: 5470 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: NO RESTRAINTS ON DISTANCES AND ANGLES
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.026
RfactorNum. reflection% reflectionSelection details
Rfree0.097 1568 10 %RANDOM
all0.081 15653 --
obs0.08 -99.4 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 286 / Occupancy sum non hydrogen: 307
Refinement stepCycle: LAST / Resolution: 0.95→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms186 0 120 1 307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.016
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_cmpnt0.024
X-RAY DIFFRACTIONs_approx_iso_adps0.032
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.0797
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d

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