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- PDB-6xa2: Structure of the tirandamycin C-bound P450 monooxygenase TamI -

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Basic information

Entry
Database: PDB / ID: 6xa2
TitleStructure of the tirandamycin C-bound P450 monooxygenase TamI
ComponentsTamI
KeywordsOXIDOREDUCTASE / P450 / Monooxygenase
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 / Chem-V0A / TamI
Similarity search - Component
Biological speciesStreptomyces sp. 307-9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsNewmister, S.A. / Srivastava, K.R. / Espinoza, R.V. / Haatveit, K.C. / Khatri, Y. / Martini, R.M. / Garcia-Borras, M. / Podust, L.M. / Houk, K.N. / Sherman, D.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1700982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM118101 United States
CitationJournal: Acs Catalysis / Year: 2020
Title: Molecular Basis of Iterative C─H Oxidation by TamI, a Multifunctional P450 monooxygenase from the Tirandamycin Biosynthetic Pathway.
Authors: Newmister, S.A. / Srivastava, K.R. / Espinoza, R.V. / Haatveit, K.C. / Khatri, Y. / Martini, R.M. / Garcia-Borras, M. / Podust, L.M. / Houk, K.N. / Sherman, D.H.
History
DepositionJun 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TamI
B: TamI
C: TamI
D: TamI
E: TamI
F: TamI
G: TamI
H: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,71224
Polymers365,6978
Non-polymers8,01616
Water3,981221
1
A: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7143
Polymers45,7121
Non-polymers1,0022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7143
Polymers45,7121
Non-polymers1,0022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7143
Polymers45,7121
Non-polymers1,0022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7143
Polymers45,7121
Non-polymers1,0022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7143
Polymers45,7121
Non-polymers1,0022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7143
Polymers45,7121
Non-polymers1,0022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7143
Polymers45,7121
Non-polymers1,0022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7143
Polymers45,7121
Non-polymers1,0022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.554, 57.156, 282.659
Angle α, β, γ (deg.)90.000, 90.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TamI


Mass: 45712.086 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. 307-9 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D3Y1J3
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-V0A / (3E)-3-{(2E,4E,6R)-1-hydroxy-4-methyl-6-[(1R,3R,4S,5R)-1,4,8-trimethyl-2,9-dioxabicyclo[3.3.1]non-7-en-3-yl]hepta-2,4-dien-1-ylidene}-2H-pyrrole-2,4(3H)-dione / Tirandamycin C


Mass: 385.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H27NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 0.9 M sodium chloride, 0.1 M bis-tris pH 6.5, 2.5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0334 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2017
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0334 Å / Relative weight: 1
ReflectionResolution: 2.64→48.55 Å / Num. obs: 106833 / % possible obs: 99.76 % / Redundancy: 13.3 % / Biso Wilson estimate: 45.4 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.24 / Rrim(I) all: 0.25 / Net I/σ(I): 10.6
Reflection shellResolution: 2.64→2.734 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.76 / Num. unique obs: 10575 / CC1/2: 0.682 / CC star: 0.901 / Rrim(I) all: 1.5 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
XDSdata scaling
JBluIce-EPICSdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TamI

Resolution: 2.64→48.55 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2988 1999 1.87 %
Rwork0.2517 104834 -
obs0.2526 106833 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.29 Å2 / Biso mean: 51.623 Å2 / Biso min: 17.65 Å2
Refinement stepCycle: final / Resolution: 2.64→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24302 0 568 221 25091
Biso mean--41.93 38.32 -
Num. residues----3185
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.64-2.70.38051330.33967259739297
2.7-2.770.41181470.344673637510100
2.77-2.860.36781390.330875037642100
2.86-2.950.37331400.326973967536100
2.95-3.050.3471440.292874577601100
3.05-3.180.30121430.280275067649100
3.18-3.320.29461380.26974407578100
3.32-3.50.30291440.266474567600100
3.5-3.710.33451390.251274857624100
3.71-40.27551460.230274977643100
4-4.40.25111440.217775637707100
4.4-5.040.24321450.209375327677100
5.04-6.350.30821480.24676027750100
6.35-48.550.27981490.21397775792499

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