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- PDB-6l39: Cytochrome P450 107G1 (RapN) -

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Basic information

Entry
Database: PDB / ID: 6l39
TitleCytochrome P450 107G1 (RapN)
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
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces rapamycinicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsKim, 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)91,9058
Polymers90,2702
Non-polymers1,6356
Water724
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9644
Polymers45,1351
Non-polymers8293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9414
Polymers45,1351
Non-polymers8063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.978, 99.798, 62.684
Angle α, β, γ (deg.)90.000, 89.820, 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) / Strain (production host): BL21(DE3) / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: 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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M imidazole pH 8.0 1 M sodium citrate

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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: 2.9→50 Å / Num. obs: 39493 / % possible obs: 96.6 % / Redundancy: 2.8 % / CC1/2: 0.949 / Net I/σ(I): 8.6
Reflection shellResolution: 2.9→2.95 Å / Mean I/σ(I) obs: 8.6 / Num. unique obs: 39493 / CC1/2: 0.949

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Processing

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

4z5p


Resolution: 2.97→32.77 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.837 / SU B: 0.017 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.398 / ESU R Free: 0.63 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3132 997 6.8 %RANDOM
Rwork0.1975 ---
obs0.2049 13728 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.65 Å2 / Biso mean: 69.884 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.04 Å2
2--0.02 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.97→32.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5915 0 110 4 6029
Biso mean--63.83 52.78 -
Num. residues----759
LS refinement shellResolution: 2.972→3.049 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 45 -
Rwork0.278 734 -
all-779 -
obs--70.18 %

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