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- PDB-6kzs: Crystal structure of cytochrome P450mel 107F1 in complex with hem... -

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Basic information

Entry
Database: PDB / ID: 6kzs
TitleCrystal structure of cytochrome P450mel 107F1 in complex with heme and imidazole
ComponentsCytochrome P-450
KeywordsOXIDOREDUCTASE / biaryl coupling / Heme / 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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsHou, X.D. / Rao, Y.J. / Icyishaka, P. / Li, C.X. / Lou, J.L.
Funding support China, 3items
OrganizationGrant numberCountry
Other privateBK20160167 China
Other privateJUSRP51712B China
Other private2018YFA090170 China
CitationJournal: To Be Published
Title: Crystallization and X-ray analysis of cytochrome P450mel 107F1 with biaryl coupling reactivity
Authors: Hou, X.D. / Rao, Y.J. / Icyishaka, P. / Li, C.X. / Lou, J.L. / Liu, C.M.
History
DepositionSep 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 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 P-450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3233
Polymers46,6371
Non-polymers6862
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-21 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.699, 81.395, 100.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P-450 / Cytochrome P450


Mass: 46636.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: P-450mel, p450-mel, NCTC13033_01802 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4H2B8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride hexahydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 53190 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.022 / Rrim(I) all: 0.081 / Χ2: 0.968 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6313.20.44126180.9660.1260.4590.586100
1.63-1.6613.20.39326120.9680.1120.4090.609100
1.66-1.6913.20.35926130.9770.1020.3730.632100
1.69-1.7213.10.31826280.9790.0910.3310.662100
1.72-1.7612.80.28526180.980.0820.2970.708100
1.76-1.812.70.25126180.9810.0730.2620.753100
1.8-1.85120.21726250.9810.0650.2270.827100
1.85-1.912.30.18626350.9870.0550.1940.91100
1.9-1.9513.20.17426230.990.050.1821.009100
1.95-2.0213.40.15626560.9920.0440.1621.087100
2.02-2.0913.30.13626180.9930.0390.1411.141100
2.09-2.1713.30.11526220.9940.0330.121.118100
2.17-2.27130.10126590.9960.0290.1061.126100
2.27-2.3912.20.09126640.9970.0270.0951.102100
2.39-2.5413.10.08226510.9980.0230.0851.088100
2.54-2.7413.60.07526750.9970.0210.0781.116100
2.74-3.0113.40.06626790.9980.0190.0691.165100
3.01-3.4512.40.05926950.9980.0170.0621.309100
3.45-4.3413.10.04827400.9990.0140.051.295100
4.34-5012.10.04428750.9990.0130.0461.07399.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2d09

2d09


Resolution: 1.601→43.824 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.63
RfactorNum. reflection% reflection
Rfree0.2068 2663 5.01 %
Rwork0.1861 --
obs0.1871 53190 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.13 Å2 / Biso mean: 16.0439 Å2 / Biso min: 5.71 Å2
Refinement stepCycle: final / Resolution: 1.601→43.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 48 177 3358
Biso mean--9.23 20.39 -
Num. residues----396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.601-1.63010.22161210.1857245592
1.6301-1.66150.23011460.18682610100
1.6615-1.69540.21141360.18432649100
1.6954-1.73230.20951510.18042613100
1.7323-1.77260.24341440.18042626100
1.7726-1.81690.20511420.18032640100
1.8169-1.8660.22181360.1862651100
1.866-1.92090.20691450.18242602100
1.9209-1.98290.22261580.1812645100
1.9829-2.05380.19541350.18392662100
2.0538-2.13610.21461200.18162653100
2.1361-2.23330.23231330.18332693100
2.2333-2.3510.20871350.19072658100
2.351-2.49830.24321470.19662670100
2.4983-2.69120.21271350.19992677100
2.6912-2.96190.21091520.20072692100
2.9619-3.39040.19371440.19882709100
3.3904-4.27090.18361440.172733100

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