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- PDB-2y98: Structure of the mixed-function P450 MycG in complex with mycinam... -

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Basic information

Entry
Database: PDB / ID: 2y98
TitleStructure of the mixed-function P450 MycG in complex with mycinamicin IV in P21212 space group
ComponentsP-450-LIKE PROTEIN
KeywordsOXIDOREDUCTASE / MYCINAMICIN BIOSYNTHESIS
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLi, S. / Kells, P.M. / Sherman, D.H. / Podust, L.M.
CitationJournal: 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
DepositionFeb 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P-450-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2818
Polymers46,5571
Non-polymers1,7247
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.285, 162.025, 50.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein P-450-LIKE PROTEIN / MYCG


Mass: 46556.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MICROMONOSPORA GRISEORUBIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59523

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Non-polymers , 6 types, 404 molecules

#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE BOND TO CYS 346 MYCINAMICIN IV (MIV): NATIVE ...PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE BOND TO CYS 346 MYCINAMICIN IV (MIV): NATIVE MYCG SUBSTRATE GLYCEROL (GOL): PART OF CRYO-PROTECTANT
Sequence detailsTHE 6XHIS TAG AND THROMBIN CLEAVAGE SITE ARE ENGINEERED AT THE N-TERMINUS

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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: 2.45 Å3/Da / Density % sol: 49.7 % / Description: NONE
Crystal growTemperature: 296 K / pH: 5.5
Details: 8% PEG 4000, 0.2 M AMMONIUM SULFATE, 0.1 M BISTRIS PH 5.5, TEMP 23 C

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2009 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.65→81.01 Å / Num. obs: 47944 / % possible obs: 84.9 % / Observed criterion σ(I): 1.5 / Redundancy: 6.4 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.6 / % possible all: 40.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z36

2z36


Resolution: 1.65→162.02 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.521 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20611 2432 5.1 %RANDOM
Rwork0.14785 ---
obs0.15075 45438 84.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.986 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2--2.78 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.65→162.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 115 397 3596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1732.0374661
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.59122.468158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23215538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2511542
X-RAY DIFFRACTIONr_chiral_restr0.1510.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212655
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0941.52054
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1323329
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.28831347
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.44.51332
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.71533401
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 61 -
Rwork0.412 1341 -
obs--34.24 %

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