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- PDB-5nws: Crystal structure of saAcmM involved in actinomycin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 5nws
TitleCrystal structure of saAcmM involved in actinomycin biosynthesis
ComponentssaAcmM
KeywordsBIOSYNTHETIC PROTEIN / actinomycin / P450
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.227 Å
AuthorsDriller, R. / Semsary, S. / Crnovicic, I. / Vater, J. / Keller, U. / Loll, B.
CitationJournal: Chembiochem / Year: 2018
Title: Ketonization of Proline Residues in the Peptide Chains of Actinomycins by a 4-Oxoproline Synthase.
Authors: Semsary, S. / Crnovcic, I. / Driller, R. / Vater, J. / Loll, B. / Keller, U.
History
DepositionMay 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: saAcmM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3915
Polymers48,3961
Non-polymers9954
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-22 kcal/mol
Surface area17290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.254, 129.539, 111.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-771-

HOH

21A-798-

HOH

31A-800-

HOH

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Components

#1: Protein saAcmM


Mass: 48396.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S9NIH4*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 17.5% (w/v) polyethylene glycol 6000 100 mM Tris/HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.5 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2015
RadiationMonochromator: SI111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.227→43.04 Å / Num. obs: 54229 / % possible obs: 99.7 % / Redundancy: 6.5 % / Net I/σ(I): 11.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A4H

3a4h


Resolution: 2.227→43.037 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.55
RfactorNum. reflection% reflection
Rfree0.2195 2097 3.87 %
Rwork0.1783 --
obs0.1799 54218 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.227→43.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 65 231 3430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113308
X-RAY DIFFRACTIONf_angle_d1.1184513
X-RAY DIFFRACTIONf_dihedral_angle_d12.7191992
X-RAY DIFFRACTIONf_chiral_restr0.053490
X-RAY DIFFRACTIONf_plane_restr0.007594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2266-2.27840.31281360.24963343X-RAY DIFFRACTION95
2.2784-2.33540.25921390.23683460X-RAY DIFFRACTION100
2.3354-2.39850.24521400.22943488X-RAY DIFFRACTION100
2.3985-2.46910.27771390.21643488X-RAY DIFFRACTION100
2.4691-2.54880.28351440.20923504X-RAY DIFFRACTION100
2.5488-2.63980.27181370.19143460X-RAY DIFFRACTION100
2.6398-2.74550.2241400.19133493X-RAY DIFFRACTION100
2.7455-2.87040.23281380.1893477X-RAY DIFFRACTION100
2.8704-3.02170.22871430.18633511X-RAY DIFFRACTION100
3.0217-3.2110.25261420.193459X-RAY DIFFRACTION100
3.211-3.45880.19411360.16463496X-RAY DIFFRACTION100
3.4588-3.80670.20541400.1653481X-RAY DIFFRACTION100
3.8067-4.35710.21221440.14153477X-RAY DIFFRACTION100
4.3571-5.48770.16651420.14963489X-RAY DIFFRACTION100
5.4877-43.0450.19491370.18163495X-RAY DIFFRACTION100

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