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

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Basic information

Entry
Database: PDB / ID: 4pxh
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


cholest-4-en-3-one 26-monooxygenase activity / amino acid activation for nonribosomal peptide biosynthetic process / steroid hydroxylase activity / cholesterol catabolic process / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / iron ion binding ...cholest-4-en-3-one 26-monooxygenase activity / amino acid activation for nonribosomal peptide biosynthetic process / steroid hydroxylase activity / cholesterol catabolic process / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / ACP-like / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. ...Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / ACP-like / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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 24, 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 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P450 monooxygenase
B: Peptide synthetase
C: P450 monooxygenase
D: Peptide synthetase
E: P450 monooxygenase
F: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,87412
Polymers178,6676
Non-polymers3,2076
Water1,31573
1
A: P450 monooxygenase
B: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6254
Polymers59,5562
Non-polymers1,0692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-36 kcal/mol
Surface area21120 Å2
MethodPISA
2
C: P450 monooxygenase
D: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6254
Polymers59,5562
Non-polymers1,0692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-35 kcal/mol
Surface area20780 Å2
MethodPISA
3
E: P450 monooxygenase
F: Peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6254
Polymers59,5562
Non-polymers1,0692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-35 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.700, 161.700, 337.490
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: 49369.414 Da / Num. of mol.: 3
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.: 3 / Fragment: peptidyl carrier protein domain
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.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: C15H25N4O8PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
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: 3.56 Å3/Da / Density % sol: 65.49 %
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: 1.00002 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: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.7→47.893 Å / Num. all: 72148 / Num. obs: 72098 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 19.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 24.5
Reflection shellResolution: 2.7→3 Å / Redundancy: 19.9 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PWV

4pwv


Resolution: 2.7→47.893 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.913 / SU B: 19.736 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24598 3577 5 %RANDOM
Rwork0.2145 ---
obs0.21608 68521 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: 54.081 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11443 0 213 73 11729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211932
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.871.99916256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.31151454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95723.67575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68115.0231925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.09915107
X-RAY DIFFRACTIONr_chiral_restr0.0580.21803
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219179
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_it0.1731.57262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.333211712
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.49234670
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8424.54539
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 231 -
Rwork0.27 4981 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2563-0.64320.81192.8953-0.37931.9209-0.07680.13750.16880.16090.0018-0.2148-0.05630.22450.07510.03560.0098-0.01420.14280.09210.0907-33.331569.978-13.7048
211.8302-5.01839.52723.9613-4.124215.76830.38231.0293-0.0003-0.1395-0.498-0.16160.61471.11560.11570.27820.1373-0.06420.4210.15320.1515-9.584559.147211.0096
31.10170.5139-0.40253.3203-0.37761.4469-0.0299-0.0286-0.1625-0.2010.0069-0.10240.12540.12860.0230.1018-0.0058-0.01870.05030.0460.0794-31.7749115.319212.2987
414.15445.5886-11.533.3256-3.844216.66270.2265-0.18610.1587-0.1261-0.15980.047-0.15980.2067-0.06670.2650.03670.07670.16650.12010.1553-7.073128.7556-9.9663
53.0877-0.40820.74511.83370.16722.4628-0.2182-0.29720.434-0.04860.06960.2481-0.2893-0.29940.14870.11830.0093-0.13850.13910.00570.23-76.6339101.129440.823
69.45815.16196.74017.02476.080215.1487-0.46120.12610.159-0.05880.39490.0856-0.3350.39370.06620.34510.024-0.21360.2698-0.08370.2835-53.673115.894664.0012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 423
2X-RAY DIFFRACTION2B6 - 80
3X-RAY DIFFRACTION3C11 - 419
4X-RAY DIFFRACTION4D6 - 79
5X-RAY DIFFRACTION5E11 - 417
6X-RAY DIFFRACTION6F6 - 79

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