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- PDB-2c6h: Crystal structure of YC-17-bound cytochrome P450 PikC (CYP107L1) -

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Basic information

Entry
Database: PDB / ID: 2c6h
TitleCrystal structure of YC-17-bound cytochrome P450 PikC (CYP107L1)
ComponentsCYTOCHROME P450 MONOOXYGENASE
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / PIKC / CYP107L1 / MACROLIDE MONOOXYGENASE / ANTIBIOTIC BIOSYNTHESIS / HEME / IRON / METAL-BINDING / MONOOXYGENASE / OXIDOREDUCTASE ANTIBIOTIC BIOSYNTHESIS
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 / Chem-PXI / Cytochrome P450 monooxygenase PikC
Similarity search - Component
Biological speciesSTREPTOMYCES VENEZUELAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 9, 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 1.3Dec 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
B: CYTOCHROME P450 MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,15811
Polymers96,5372
Non-polymers2,6219
Water3,891216
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A: CYTOCHROME P450 MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7237
Polymers48,2691
Non-polymers1,4546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME P450 MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4354
Polymers48,2691
Non-polymers1,1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.457, 104.700, 153.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99983, 0.0182, 0.00149), (-0.0178, 0.98968, -0.14219), (-0.00406, 0.14214, 0.98984)
Vector: -42.15639, -41.77388, -3.07427)

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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.: 2
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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PXI / 4-{[4-(DIMETHYLAMINO)-3-HYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-12-ETHYL-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE


Mass: 453.612 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H43NO6
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growpH: 6.5
Details: 30% PEG MME 5000, 0.1 M MES, 6.5, 0.5 MM DTT, 0.2 M AMMONIUM SULFATE, 1 MM YC-17, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.72196
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2005
Details: SAGITTAL FOCUSING CRYSTAL AND VERTICALLY FOCUSING DOUBLE MIRROR
RadiationMonochromator: SI (220) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.72196 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 41228 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.3 / % possible all: 95.8

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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: 2.35→49.56 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 377379.43 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE OMMITED FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.231 7162 9.8 %RANDOM
Rwork0.195 ---
obs0.195 72999 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3702 Å2 / ksol: 0.365531 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--3.29 Å20 Å2
3----3.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.35→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6101 0 175 216 6492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 1090 10.3 %
Rwork0.261 9489 -
obs--80.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4YC17_NEW.PARYC17_NEW.TOP

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