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- PDB-2c7x: Crystal structure of narbomycin-bound cytochrome P450 PikC (CYP107L1) -

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Basic information

Entry
Database: PDB / ID: 2c7x
TitleCrystal structure of narbomycin-bound cytochrome P450 PikC (CYP107L1)
ComponentsCYTOCHROME P450 MONOOXYGENASE
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / PIKC / NARBOMYCIN / MACROLIDE MONOOXYGENASE / ANTIBIOTIC BIOSYNTHESIS / HEME / IRON / METAL-BINDING / MONOOXYGENASE
Function / homology
Function and homology information


pikromycin synthase / macrolide 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 / NARBOMYCIN / Cytochrome P450 monooxygenase PikC
Similarity search - Component
Biological speciesSTREPTOMYCES VENEZUELAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSherman, D.H. / Li, S. / Yermalitskaya, L.V. / Kim, Y. / Smith, J.A. / Waterman, M.R. / Podust, L.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Structural Basis for Substrate Anchoring, Active Site Selectivity, and Product Formation by P450 Pikc from Streptomyces Venezuelae.
Authors: Sherman, D.H. / Li, S. / Yermalitskaya, L.V. / Kim, Y. / Smith, J.A. / Waterman, M.R. / Podust, L.M.
History
DepositionNov 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 13, 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_conn
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_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_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.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450 MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3953
Polymers48,2691
Non-polymers1,1262
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.963, 64.896, 92.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME P450 MONOOXYGENASE / CYTOCHROME P450 PIKC CYP107L1 / CYTOCHROME P450 HYDROXYLASE PIKC


Mass: 48268.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES VENEZUELAE (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: O87605
#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-NRB / NARBOMYCIN


Mass: 509.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H47NO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 20 RESIDUES INCLUDING 6X HIS-TAG AND THROMBIN CLEAVAGE SITE ARE FROM THE CLONING VECTOR PET28A

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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: 1.9 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 293 K / pH: 6
Details: 0.1 M MES, 6.0 0.8 M AMMONIUM SULFATE, 0.5 MM DTT, 1 MM NARBOMYCIN, T=20 C, pH 6.00

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97952
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 28, 2005
Details: SAGITTAL FOCUSING CRYSTAL AND VERTICAL FOCUSING DOUBLE MIRROR
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 36334 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 65.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.6 / % possible all: 80.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVJ

2bvj


Resolution: 1.75→49.77 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 329931.62 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: DISORDERED REGIONS WERE OMMITED FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3408 10 %RANDOM
Rwork0.207 ---
obs0.207 34218 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1004 Å2 / ksol: 0.369607 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--7.41 Å20 Å2
3----7.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.75→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 79 166 3296
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 420 9.6 %
Rwork0.275 3940 -
obs--72.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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