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- PDB-6vdp: Crystal structure of SfmD truncated variant -

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Basic information

Entry
Database: PDB / ID: 6vdp
TitleCrystal structure of SfmD truncated variant
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 / MAD / Resolution: 2 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 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Water1,33374
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)59.863, 59.863, 155.848
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 41.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl pH 8.5, 0.2 M magnesium chloride, 20% PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22661 / % possible obs: 99.9 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.022 / Rrim(I) all: 0.098 / Χ2: 0.901 / Net I/σ(I): 6.9 / Num. measured all: 433971
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0717.71.68922020.7530.4091.7390.78799.9
2.07-2.1520.21.06422070.8870.241.0910.778100
2.15-2.2519.90.6922300.9390.1570.7070.826100
2.25-2.3719.40.43622380.9760.10.4480.814100
2.37-2.52180.31522340.9840.0760.3240.85399.9
2.52-2.7120.30.20422530.9940.0460.2090.88699.9
2.71-2.9919.80.13522670.9970.0310.1390.934100
2.99-3.4218.70.08922560.9980.0210.0910.99899.9
3.42-4.3119.70.06123190.9990.0140.0630.969100
4.31-5017.80.06724550.9980.0160.0691.15499.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→49.19 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 2012 8.9 %
Rwork0.1963 20602 -
obs0.2004 22614 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.95 Å2 / Biso mean: 46.1529 Å2 / Biso min: 27.28 Å2
Refinement stepCycle: final / Resolution: 2→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 43 74 2365
Biso mean--43.4 47.25 -
Num. residues----304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.050.3241400.26214011541
2.05-2.110.30281450.240414551600
2.11-2.170.31621410.224314451586
2.17-2.240.31031390.220514361575
2.24-2.320.26471440.205114631607
2.32-2.410.28021460.207814481594
2.41-2.520.25271380.197814631601
2.52-2.650.25681440.204514521596
2.65-2.820.26821460.203814501596
2.82-3.040.23361440.216614911635
3.04-3.340.26731410.221614811622
3.34-3.830.22681440.187914891633
3.83-4.820.2151470.180715171664
4.82-49.190.22951530.179116111764

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