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- PDB-5ysw: Crystal Structure Analysis of Rif16 in complex with R-L -

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Basic information

Entry
Database: PDB / ID: 5ysw
TitleCrystal Structure Analysis of Rif16 in complex with R-L
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / rifamycin / METAL BINDING PROTEIN
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 / 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
Chem-9LF / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesAmycolatopsis mediterranei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, F.W. / Qi, F.F. / Xiao, Y.L. / Zhao, G.P. / Li, S.Y.
CitationJournal: Nat Commun / Year: 2018
Title: Deciphering the late steps of rifamycin biosynthesis.
Authors: Qi, F. / Lei, C. / Li, F. / Zhang, X. / Wang, J. / Zhang, W. / Fan, Z. / Li, W. / Tang, G.L. / Xiao, Y. / Zhao, G. / Li, S.
History
DepositionNov 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1583
Polymers48,7851
Non-polymers1,3722
Water1,15364
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 area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.082, 70.709, 80.975
Angle α, β, γ (deg.)90.000, 94.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 48785.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei (strain U-32) (bacteria)
Strain: U-32 / Gene: AMED_0653 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3CVZ6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-9LF / (2S,12E,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-(acetyloxy)-5,6,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-9-yl hydroxyacetate / Rifamycin L


Mass: 755.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H49NO14
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 42.93 % / Mosaicity: 1.48 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5 / Details: Magnesium chloride hexahydrate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.976 Å
DetectorType: SIEMENS-NICOLET / Detector: CCD / Date: Nov 3, 2017 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 12806 / % possible obs: 98.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.049 / Rrim(I) all: 0.12 / Χ2: 0.968 / Net I/σ(I): 5.7 / Num. measured all: 74314
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.645.70.55512650.8330.2470.6090.92299.3
2.64-2.755.40.44112620.8760.2030.4870.8997.5
2.75-2.875.50.3712760.9070.1690.4080.9399
2.87-3.0260.29612600.9440.1280.3230.92397.6
3.02-3.216.10.21612610.9760.0930.2350.93896.9
3.21-3.4660.14912710.9840.0650.1630.9798.8
3.46-3.815.80.10312720.990.0460.1130.98898.6
3.81-4.365.50.07413040.9940.0340.0821.07699.8
4.36-5.496.30.06412970.9960.0280.071.055100
5.49-505.80.05813380.9970.0260.0640.97599.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OQS

4oqs


Resolution: 2.6→35.38 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.2532 / WRfactor Rwork: 0.1937 / FOM work R set: 0.8123 / SU B: 11.814 / SU ML: 0.261 / SU Rfree: 0.3772 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 580 4.9 %RANDOM
Rwork0.2052 ---
obs0.2085 11248 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.87 Å2 / Biso mean: 37.57 Å2 / Biso min: 14 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.19 Å2
2---0.59 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 2.6→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 97 64 3029
Biso mean--64.46 31.68 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193038
X-RAY DIFFRACTIONr_bond_other_d0.0050.022839
X-RAY DIFFRACTIONr_angle_refined_deg1.7042.0144159
X-RAY DIFFRACTIONr_angle_other_deg0.92436484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2785370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6922.687134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.45615449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.4661531
X-RAY DIFFRACTIONr_chiral_restr0.0990.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213450
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02692
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 37 -
Rwork0.217 717 -
all-754 -
obs--82.31 %

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