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- PDB-4pwv: Structure of P450sky (CYP163B3), a cytochrome P450 from skyllamyc... -

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Basic information

Entry
Database: PDB / ID: 4pwv
TitleStructure of P450sky (CYP163B3), a cytochrome P450 from skyllamycin biosynthesis in complex with a peptidyl carrier protein domain
Components
  • P450 monooxygenase
  • Peptide synthetase
KeywordsOXIDOREDUCTASE/PROTEIN BINDING / Cytochrome P450 fold / beta-aminoacyl carrier protein hydroxylase / peptidyl carrier protein domains / skyllamycin NRPS / OXIDOREDUCTASE-PROTEIN BINDING complex
Function / homology
Function and homology information


monocarboxylic acid biosynthetic process / cholest-4-en-3-one 26-monooxygenase activity / cholesterol catabolic process / amino acid activation for nonribosomal peptide biosynthetic process / steroid hydroxylase activity / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process ...monocarboxylic acid biosynthetic process / cholest-4-en-3-one 26-monooxygenase activity / cholesterol catabolic process / amino acid activation for nonribosomal peptide biosynthetic process / steroid hydroxylase activity / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / iron ion binding / heme binding / cytosol
Similarity search - Function
Non-ribosomal peptide synthase / Amino acid adenylation domain / Condensation domain / Condensation domain / ACP-like / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding, conserved site ...Non-ribosomal peptide synthase / Amino acid adenylation domain / Condensation domain / Condensation domain / ACP-like / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Phosphopantetheine attachment site / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Phosphopantetheine attachment site. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-KH4 / Peptide synthetase / p450 monooxygenase
Similarity search - Component
Biological speciesStreptomyces sp. Acta 2897 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsHaslinger, K. / Cryle, M.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: The structure of a transient complex of a nonribosomal Peptide synthetase and a cytochrome p450 monooxygenase.
Authors: Haslinger, K. / Brieke, C. / Uhlmann, S. / Sieverling, L. / Sussmuth, R.D. / Cryle, M.J.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_modification_feature / pdbx_nonpoly_atom_coordination ...pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P450 monooxygenase
B: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0474
Polymers59,9782
Non-polymers1,0692
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-35 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.260, 95.260, 336.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein P450 monooxygenase / cytochrome P450 sky32 (CYP163B3)


Mass: 49791.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Acta 2897 (bacteria) / Strain: Acta 2897 / Gene: sky32 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: F2YRY7, unspecific monooxygenase
#2: Protein Peptide synthetase / PCP7


Mass: 10186.228 Da / Num. of mol.: 1
Fragment: peptidyl carrier protein domain (UNP residues 3075-3154)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Acta 2897 (bacteria) / Strain: Acta 2897 / Gene: sky30 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: F2YRY5
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-KH4 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] 1H-imidazole-4-carbothioate


Mass: 452.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N4O8PS
Has protein modificationY

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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: 3.68 Å3/Da / Density % sol: 66.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350, 0.15 M calcium acetate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97968 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97968 Å / Relative weight: 1
ReflectionResolution: 3→47.63 Å / Num. all: 19079 / Num. obs: 19079 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 20.5 % / Biso Wilson estimate: 77.8 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 20.9
Reflection shellResolution: 3→3.2 Å / Redundancy: 21 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 6.5 / Num. unique all: 5998 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→47.62 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.88 / SU B: 16.742 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.876 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 955 5 %RANDOM
Rwork0.23345 ---
obs0.23555 18124 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.591 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 3→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 71 0 3888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223976
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.882.0015415
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7715484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72623.684190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70215.023639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.681535
X-RAY DIFFRACTIONr_chiral_restr0.0610.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213055
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_it0.2991.52423
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.56223908
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.59131553
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0064.51506
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 69 -
Rwork0.321 1299 -
obs-1368 100 %

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