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- PDB-6vdq: Crystal structure of SfmD -

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Basic information

Entry
Database: PDB / ID: 6vdq
TitleCrystal structure of SfmD
Components3-methyl-L-tyrosine peroxygenase
KeywordsOXIDOREDUCTASE / Heme / Hydroxylase / Histidine-ligated heme
Function / homology3-methyl-L-tyrosine peroxygenase / Tetracyclin repressor-like, C-terminal domain superfamily / antibiotic biosynthetic process / oxidoreductase activity / regulation of DNA-templated transcription / 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: 1.78 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

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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
Water3,081171
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)59.900, 59.900, 155.759
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

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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.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.7 %
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: 1.78→50 Å / Num. obs: 31968 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Χ2: 1.071 / Net I/σ(I): 10.6 / Num. measured all: 404391
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.8112.50.8815900.9110.2560.9170.355100
1.81-1.84120.74315440.9230.220.7760.38100
1.84-1.8810.90.64115910.9330.1980.6730.42299.7
1.88-1.9212.60.54515660.9490.1580.5680.714100
1.92-1.9613.30.42715530.9710.1210.4440.566100
1.96-213.20.31315870.9810.0890.3250.475100
2-2.0513.30.24515700.9890.070.2550.548100
2.05-2.11130.22515780.9890.0650.2350.882100
2.11-2.1713.20.16115620.9940.0460.1670.709100
2.17-2.2412.90.14615780.9950.0420.1520.821100
2.24-2.3212.40.13415980.9950.0390.141.195100
2.32-2.4211.20.10715880.9950.0330.1121.14299.9
2.42-2.5313.60.115940.9970.0280.1031.32299.9
2.53-2.6613.60.09115710.9970.0260.0951.43299.9
2.66-2.8313.30.08416120.9980.0240.0871.595100
2.83-3.0413.20.07616170.9980.0220.0791.70699.9
3.04-3.3512.20.06816170.9980.020.0711.812100
3.35-3.83120.0616260.9970.0180.0631.85199.9
3.83-4.83130.05416480.9980.0160.0561.67899.2
4.83-5011.70.04817780.9990.0140.0511.699.8

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Processing

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

6vdp


Resolution: 1.78→49.22 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.39
RfactorNum. reflection% reflection
Rfree0.228 1991 6.25 %
Rwork0.1992 --
obs0.2011 31878 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.47 Å2 / Biso mean: 39.902 Å2 / Biso min: 22.27 Å2
Refinement stepCycle: final / Resolution: 1.78→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 43 171 2469
Biso mean--37.87 46.36 -
Num. residues----305
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
1.78-1.820.30641410.257321172258
1.82-1.870.28741400.249420972237
1.87-1.930.28461440.243521222266
1.93-1.990.28581330.234420862219
1.99-2.060.28011390.237621052244
2.06-2.150.2551400.227221042244
2.15-2.240.27311440.225420882232
2.24-2.360.2471390.208421282267
2.36-2.510.24761440.20921302274
2.51-2.70.25971420.213221052247
2.7-2.970.25831420.217821512293
2.98-3.410.22331400.213121522292
3.41-4.290.20261440.17622032347
4.29-49.220.19911590.177422992458

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