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- PDB-2ca0: Crystal structure of YC-17-bound cytochrome P450 PikC (CYP107L1) -

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Basic information

Entry
Database: PDB / ID: 2ca0
TitleCrystal structure of YC-17-bound cytochrome P450 PikC (CYP107L1)
ComponentsCYTOCHROME P450 MONOOXYGENASE
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / PIKC / YC-17 / MACROLIDE MONOOXYGENASE / ANTIBIOTIC BIOSYNTHESIS / HEME / IRON / METAL-BINDING
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: 2.85 Å
AuthorsYermalitskaya, L.I. / Kim, Y. / Sherman, D.H. / Waterman, M.R. / Podust, L.M.
CitationJournal: To be Published
Title: Crystal Structure of Yc-17-Bound Cytochrome P450 Pikc (Cyp107L1)
Authors: Yermalitskaya, L.I. / Kim, Y. / Sherman, D.H. / Waterman, M.R. / Podust, L.M.
History
DepositionDec 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 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

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Assembly

Deposited unit
A: CYTOCHROME P450 MONOOXYGENASE
B: CYTOCHROME P450 MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6786
Polymers96,5372
Non-polymers2,1404
Water1,13563
1
A: CYTOCHROME P450 MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3393
Polymers48,2691
Non-polymers1,0702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME P450 MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3393
Polymers48,2691
Non-polymers1,0702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.088, 91.972, 68.901
Angle α, β, γ (deg.)90.00, 89.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99882, 0.03381, -0.03492), (-0.03478, -0.99902, 0.02749), (-0.03396, 0.02867, 0.99901)
Vector: 93.18421, -12.06961, 31.93128)

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Components

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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.21 Å3/Da / Density % sol: 43.79 %
Crystal growpH: 6.5
Details: 10% PEG MME 5000,0.1 M MES 6.5, 0.1 M AMMONIUM SULFATE, 0.5 MM DTT 1 MM YC-17, pH 6.50

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Data collection

DiffractionMean temperature: 100 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: 2.85→50 Å / Num. obs: 17855 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 75.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.1
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.8 / % possible all: 75.8

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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: 2.85→32.41 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 124191.07 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.338 1661 10.1 %RANDOM
Rwork0.24 ---
obs0.24 16518 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1387 Å2 / ksol: 0.333374 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.69 Å20 Å2-9.49 Å2
2---5.25 Å20 Å2
3----3.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.85→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 150 63 6269
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.422
X-RAY DIFFRACTIONc_scangle_it2.192.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 237 10.7 %
Rwork0.318 1983 -
obs--74.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1WATER_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.TOP

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