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- PDB-6xa3: Structure of the ligand free P450 monooxygenase TamI -

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Basic information

Entry
Database: PDB / ID: 6xa3
TitleStructure of the ligand free 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 / TamI
Similarity search - Component
Biological speciesStreptomyces sp. 307-9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 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 23, 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 1.2Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: TamI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7062
Polymers49,0901
Non-polymers6161
Water34219
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)154.498, 154.498, 91.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein TamI


Mass: 49089.602 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 3.5 M sodium formate, pH 7.0 and 0.1 M strontium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2009
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.96→21.16 Å / Num. obs: 11821 / % possible obs: 99.7 % / Redundancy: 10.7 % / Biso Wilson estimate: 69.35 Å2 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.139 / Net I/σ(I): 15
Reflection shellResolution: 2.96→3.12 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1689 / Rrim(I) all: 1.04 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
Cootmodel building
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bvj

2bvj


Resolution: 2.96→21.16 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3132 563 4.76 %
Rwork0.2544 11256 -
obs0.2573 11819 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.04 Å2 / Biso mean: 66.6463 Å2 / Biso min: 34.26 Å2
Refinement stepCycle: final / Resolution: 2.96→21.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 43 19 3176
Biso mean--47.68 49.23 -
Num. residues----409
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
2.96-3.260.40171390.336527582897
3.26-3.730.36071410.296627662907
3.73-4.690.3241460.247328032949
4.69-21.160.25941370.220829293066

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