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- PDB-6kzt: Crystal structure of cytochrome P450mel 107F1 with biaryl couplin... -

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Basic information

Entry
Database: PDB / ID: 6kzt
TitleCrystal structure of cytochrome P450mel 107F1 with biaryl coupling reactivity
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 / Cytochrome P-450
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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)47,2532
Polymers46,6371
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.508, 117.508, 75.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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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
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: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 18% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 20% w/v Polyethylene glycol 4000

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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 S 6M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 7557 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.054 / Rrim(I) all: 0.242 / Χ2: 0.986 / Net I/σ(I): 3.5 / Num. measured all: 151136
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.5620.90.5543830.9690.1240.5670.849100
3.56-3.6321.40.4943700.9560.1090.5060.923100
3.63-3.6921.20.4293670.9520.0960.4391.288100
3.69-3.7720.80.3873900.970.0870.3971.054100
3.77-3.8520.80.4793610.9840.1080.4910.92100
3.85-3.9420.20.4793720.9830.1090.4921.043100
3.94-4.0420.40.3173820.990.0720.3260.841100
4.04-4.1520.20.2743740.9920.0620.2810.885100
4.15-4.2719.90.3273630.9860.0750.3351.042100
4.27-4.4119.40.2463840.980.0570.2531.794100
4.41-4.5719.10.2313680.9930.0540.2371.069100
4.57-4.7519.20.2023740.9940.0470.2070.957100
4.75-4.9718.50.1853860.9940.0440.190.821100
4.97-5.2316.30.1963740.9920.050.2030.825100
5.23-5.5516.90.2183770.9930.0540.2240.825100
5.55-5.98200.2193820.9920.050.2240.843100
5.98-6.5822.40.2293810.9940.0490.2340.858100
6.58-7.5321.90.1673810.9960.0360.1711.021100
7.53-9.4821.90.0783880.9990.0170.080.865100
9.48-5018.70.0564000.9990.0130.0570.98899.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2d09

2d09


Resolution: 3.5→42.17 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.85 / SU B: 31.062 / SU ML: 0.464 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.699 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2814 735 9.8 %RANDOM
Rwork0.1882 ---
obs0.1968 6784 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.23 Å2 / Biso mean: 49.89 Å2 / Biso min: 27.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å2-0 Å2
3----0.66 Å2
Refinement stepCycle: final / Resolution: 3.5→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 43 0 3176
Biso mean--37.1 --
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133251
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173059
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.6824440
X-RAY DIFFRACTIONr_angle_other_deg1.1981.5857047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.725395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84519.686191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33715536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1911541
X-RAY DIFFRACTIONr_chiral_restr0.0610.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023659
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02732
LS refinement shellResolution: 3.505→3.596 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 63 -
Rwork0.217 481 -
all-544 -
obs--98.19 %

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