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- PDB-6l3a: Cytochrome P450 107G1 (RapN) with everolimus -

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Basic information

Entry
Database: PDB / ID: 6l3a
TitleCytochrome P450 107G1 (RapN) with everolimus
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450
Function / homology
Function and homology information


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 superfamily / Cytochrome P450
Similarity search - Domain/homology
Everolimus / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces rapamycinicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKm, V.C. / Kim, D.H. / Lim, Y.R. / Lee, I.H. / Lee, J.H. / Kang, L.W.
CitationJournal: Arch.Biochem.Biophys. / Year: 2020
Title: Structural insights into CYP107G1 from rapamycin-producing Streptomyces rapamycinicus.
Authors: Kim, V. / Lim, Y.R. / Lee, I. / Lee, J.H. / Han, S. / Pham, T.V. / Kim, H. / Lee, R. / Kang, L.W. / Kim, D.
History
DepositionOct 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4615
Polymers90,2702
Non-polymers2,1913
Water724
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7512
Polymers45,1351
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7103
Polymers45,1351
Non-polymers1,5752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.028, 126.142, 70.099
Angle α, β, γ (deg.)90.000, 116.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / RapN


Mass: 45134.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rapamycinicus (strain ATCC 29253 / DSM 41530 / NRRL 5491 / AYB-994) (bacteria)
Strain: ATCC 29253 / DSM 41530 / NRRL 5491 / AYB-994 / Gene: D3C57_102975 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A0NSZ7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-E53 / Everolimus / (1S,9R,12S,15R,16E,18R,19S,21R,23S,24Z,26Z,28Z,30R,32R,35S)-12-[(2S)-1-[(1S,3S,4R)-4-(2-hydroxyethyloxy)-3-methoxy-cyclohexyl]propan-2-yl]-19,30-dimethoxy-15,17,21,23,29,35-hexamethyl-1,18-bis(oxidanyl)-11,36-dioxa-4-azatricyclo[30.3.1.0^{4,9}]hexatriaconta-16,24,26,28-tetraene-2,3,10,14,20-pentone


Mass: 958.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C53H83NO14 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate, 0.2 M magnesium acetate tetrahydrate, 20% polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 41761 / % possible obs: 97.3 % / Redundancy: 3.2 % / CC1/2: 0.89 / Net I/σ(I): 18.3
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 18.3 / Num. unique obs: 41761 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z5P

4z5p


Resolution: 3→44.49 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.845 / SU B: 34.474 / SU ML: 0.574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.601
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3355 1055 5.4 %RANDOM
Rwork0.2406 ---
obs0.2457 18426 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 218.85 Å2 / Biso mean: 74.729 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.04 Å2
2---0.03 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 3→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 154 4 6240
Biso mean--98.04 49.16 -
Num. residues----783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136424
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176186
X-RAY DIFFRACTIONr_angle_refined_deg1.631.6878751
X-RAY DIFFRACTIONr_angle_other_deg1.1441.60314295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2765778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85320.738325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.654151100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4381559
X-RAY DIFFRACTIONr_chiral_restr0.0650.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027072
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021330
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 77 -
Rwork0.449 1375 -
all-1452 -
obs--99.52 %

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