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- PDB-2yca: Mixed-function P450 MycG in complex with mycinamicin III in P2121... -

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Basic information

Entry
Database: PDB / ID: 2yca
TitleMixed-function P450 MycG in complex with mycinamicin III 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 / antibiotic biosynthetic process / 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 / 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 / SUCCINIC ACID / MYCINAMICIN III / Mycinamicin IV hydroxylase/epoxidase
Similarity search - Component
Biological speciesMICROMONOSPORA GRISEORUBIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionMar 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Dec 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,2497
Polymers46,5571
Non-polymers1,6936
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.747, 162.330, 49.789
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 , 5 types, 334 molecules

#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
#3: Chemical ChemComp-ZM3 / MYCINAMICIN III


Mass: 681.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H59NO11
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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 GLYCEROL (GOL): CRYO- ...PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE BOND TO CYS 346 GLYCEROL (GOL): CRYO-PROTECTANT MYCINAMICIN III (ZM3): BIOSYNTHETIC PRECURSOR OF NATIVE SUBSTRATES SUCCINIC ACID (SIN): PART OF CRYSTALLIZATION CONDITIONS
Sequence details6XHIS TAG AND THE THROMBIN CLEAVAGE SITE WERE 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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE
Crystal growpH: 7 / Details: 0.6 M SUCCINIC ACID, PH 7.0 .

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.8→81.17 Å / Num. obs: 43565 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y4H

2y4h
PDB Unreleased entry


Resolution: 1.8→162.33 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.238 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21027 2191 5 %RANDOM
Rwork0.15216 ---
obs0.1551 41348 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.57 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.8→162.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 117 328 3535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223391
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8752.0364637
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6235414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71622.27163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89615540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.861546
X-RAY DIFFRACTIONr_chiral_restr0.1220.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212659
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_it1.8781.52033
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.90823292
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8831358
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1464.51345
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.73533391
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 171 -
Rwork0.277 3020 -
obs--99.59 %

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