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- PDB-6xcv: Crystal structure of apo SznF from Streptomyces achromogenes var.... -

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Basic information

Entry
Database: PDB / ID: 6xcv
TitleCrystal structure of apo SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697
ComponentsCupin domain-containing diiron protein
KeywordsOXIDOREDUCTASE / diiron / N-oxygenase / N-methyl-L-arginine / heme oxygenase
Function / homology
Function and homology information


nitrosourea synthase / antibiotic biosynthetic process / monooxygenase activity / metal ion binding
Similarity search - Function
Iron-containing redox enzyme / Iron-containing redox enzyme / Cupin 2, conserved barrel / Cupin domain / Haem oxygenase-like, multi-helical / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Nitrosourea synthase
Similarity search - Component
Biological speciesStreptomyces achromogenes subsp. streptozoticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsMcBride, M.J. / Boal, A.K.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structure and assembly of the diiron cofactor in the heme-oxygenase-like domain of the N -nitrosourea-producing enzyme SznF.
Authors: McBride, M.J. / Pope, S.R. / Hu, K. / Okafor, C.D. / Balskus, E.P. / Bollinger Jr., J.M. / Boal, A.K.
History
DepositionJun 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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: Cupin domain-containing diiron protein
B: Cupin domain-containing diiron protein


Theoretical massNumber of molelcules
Total (without water)112,0852
Polymers112,0852
Non-polymers00
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-43 kcal/mol
Surface area33740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.907, 108.132, 150.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cupin domain-containing diiron protein / SznF / Iron-containing redox enzyme


Mass: 56042.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces achromogenes subsp. streptozoticus (bacteria)
Gene: stzF, sznF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A411MR89, Oxidoreductases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 16% PEG4000, 0.1 M magnesium chloride, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 92848 / % possible obs: 90.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 20.4 Å2 / CC1/2: 0.937 / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.5
Reflection shellResolution: 1.77→1.8 Å / Num. unique obs: 4473 / CC1/2: 0.698

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Processing

Software
NameVersionClassification
REFMAC1.14_3260refinement
PHENIX1.14_3260refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6M9R

6m9r


Resolution: 1.77→38.22 Å / SU ML: 0.2391 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9139 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2544 4211 5.1 %
Rwork0.2059 78365 -
obs0.2084 82576 89.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.73 Å2
Refinement stepCycle: LAST / Resolution: 1.77→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7444 0 0 592 8036
LS refinement shellResolution: 1.77→1.79 Å
RfactorNum. reflection% reflection
Rfree0.315 162 -
Rwork0.257 2457 -
obs--85.34 %

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