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- PDB-6ve0: Crystal structure of reduced SfmD by soaking with sodium hydrosulfite -

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Basic information

Entry
Database: PDB / ID: 6ve0
TitleCrystal structure of reduced SfmD by soaking with sodium hydrosulfite
Components3-methyl-L-tyrosine peroxygenase
KeywordsOXIDOREDUCTASE / Hydroxylase / Histidine-ligated heme
Function / homology3-methyl-L-tyrosine peroxygenase / Tetracyclin repressor-like, C-terminal domain superfamily / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding / HEME C / 3-methyl-L-tyrosine peroxygenase
Function and homology information
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsShin, I. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Chem Sci / Year: 2021
Title: A novel catalytic heme cofactor in SfmD with a single thioether bond and a bis -His ligand set revealed by a de novo crystal structural and spectroscopic study.
Authors: Shin, I. / Davis, I. / Nieves-Merced, K. / Wang, Y. / McHardy, S. / Liu, A.
History
DepositionDec 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-methyl-L-tyrosine peroxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8512
Polymers38,2331
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.453, 59.453, 159.965
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 3-methyl-L-tyrosine peroxygenase


Mass: 38232.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: sfmD / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B0CN28, 3-methyl-L-tyrosine peroxygenase
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 0.2 M magnesium chloride, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 6152 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.036 / Rrim(I) all: 0.109 / Χ2: 0.873 / Net I/σ(I): 6.2 / Num. measured all: 57538
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.15-3.28.61.0842950.7440.3891.1530.802100
3.2-3.2680.7872970.8530.2960.8420.79299.7
3.26-3.339.60.7393100.890.250.7810.753100
3.33-3.3910.20.6152790.920.2020.6480.79100
3.39-3.47100.4883070.9620.1610.5150.782100
3.47-3.55100.3382950.9730.1120.3560.79100
3.55-3.64100.2723050.9880.090.2870.852100
3.64-3.739.80.2473050.9880.0830.2610.871100
3.73-3.84100.2142860.9910.0710.2260.9100
3.84-3.979.70.1693210.9910.0570.1790.871100
3.97-4.119.80.1542860.9930.0520.1620.872100
4.11-4.279.60.1143180.9960.0390.1210.888100
4.27-4.479.20.1072980.9950.0380.1140.886100
4.47-4.78.40.0973070.9970.0360.1030.93999.7
4.7-58.90.093060.9970.0330.0960.9499.7
5-5.389.90.0853070.9970.0280.090.89100
5.38-5.939.70.0873190.9960.0290.0920.856100
5.93-6.789.40.0743150.9980.0250.0790.854100
6.78-8.548.70.0653340.9950.0230.0690.867100
8.54-508.10.0793620.9940.0280.0841.2799.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VDP

6vdp


Resolution: 3.15→49.01 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.18
RfactorNum. reflection% reflection
Rfree0.3077 608 9.94 %
Rwork0.2604 --
obs0.265 6117 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.05 Å2 / Biso mean: 110.441 Å2 / Biso min: 83.83 Å2
Refinement stepCycle: final / Resolution: 3.15→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 43 0 2284
Biso mean--113.01 --
Num. residues----303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.15-3.460.40191480.346113331481
3.46-3.960.37051470.307713591506
3.96-4.990.33511550.277913581513
5-49.010.26131580.224714591617

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