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- PDB-5uhu: Solution conformation of cytochrome P450 MycG with mycinamicin IV... -

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Basic information

Entry
Database: PDB / ID: 5uhu
TitleSolution conformation of cytochrome P450 MycG with mycinamicin IV bound
ComponentsMycinamicin IV hydroxylase/epoxidase
KeywordsOXIDOREDUCTASE / antibiotic biosynthesis
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / antibiotic biosynthetic process / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / MYCINAMICIN IV / Mycinamicin IV hydroxylase/epoxidase
Similarity search - Component
Biological speciesMicromonospora griseorubida (bacteria)
MethodSOLUTION NMR
AuthorsPochapsky, T.C. / Tietz, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM44191 United States
Citation
Journal: Biochemistry / Year: 2017
Title: Solution Conformations and Dynamics of Substrate-Bound Cytochrome P450 MycG.
Authors: Tietz, D.R. / Podust, L.M. / Sherman, D.H. / Pochapsky, T.C.
#1: Journal: J. Biol. Chem. / Year: 2012
Title: Substrate recognition by the multifunctional cytochrome P450 MycG in mycinamicin hydroxylation and epoxidation reactions.
Authors: Li, S. / Tietz, D.R. / Rutaganira, F.U. / Kells, P.M. / Anzai, Y. / Kato, F. / Pochapsky, T.C. / Sherman, D.H. / Podust, L.M.
History
DepositionJan 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Mycinamicin IV hydroxylase/epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6983
Polymers44,3851
Non-polymers1,3122
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-25 kcal/mol
Surface area17220 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Mycinamicin IV hydroxylase/epoxidase / Cytochrome P450 MycG / Multifunctional P450 enzyme / Mycinamicin biosynthesis protein G


Mass: 44385.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora griseorubida (bacteria) / Gene: mycG / Production host: Escherichia coli (E. coli) / Strain (production host): NCM533
References: UniProt: Q59523, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MIV / MYCINAMICIN IV


Mass: 695.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H61NO11
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic1TROSY-semiTROSY
122anisotropic1TROSY-semiTROSY
133isotropic1TROSY-semiTROSY
144isotropic13D HNCA
154isotropic13D HN(CO)CA
164isotropic13D HN(CA)CB
174isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1500 uM [U-99% 15N] MycG, 1 mM MYCINAMICIN IV, 90% H2O/10% D2OLambda phage added for magnetic alignment15N_MycMIV_pf190% H2O/10% D2O
solution2500 uM [U-99% 15N] MycG, 1 mM MYCINAMICIN IV, 90% H2O/10% D2O5% pentaethylene glycol monododecyl ether (C12E5):n-hexanol (molar ratio 0.85) for magnetic alignment15N_MycMIV_c12e590% H2O/10% D2O
solution3250 uM [U-99% 15N] MycG, 1 mM MYCINAMICIN IV, 90% H2O/10% D2Oreference, unaligned15N_MycMIV_ref90% H2O/10% D2O
solution4250 uM [U-99% 13C; U-2H on carbon;U-99% 15N] MycG, 1 mM MYCINAMICIN IV, 90% H2O/10% D2O13C_15N_2H_MycMIV90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMMycG[U-99% 15N]1
1 mMMYCINAMICIN IVnone1
500 uMMycG[U-99% 15N]2
1 mMMYCINAMICIN IVnone2
250 uMMycG[U-99% 15N]3
1 mMMYCINAMICIN IVnone3
250 uMMycG[U-99% 13C; U-2H on carbon;U-99% 15N]4
1 mMMYCINAMICIN IVnone4
Sample conditionsIonic strength: 200 mM / Ionic strength err: 0.1 / Label: conditions_1 / pH: 7.4 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
CcpNMRCCPNchemical shift assignment
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1200 / Conformers submitted total number: 1

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