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- PDB-8spp: Crystal structure of a heme enzyme RufO in rufomycin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 8spp
TitleCrystal structure of a heme enzyme RufO in rufomycin biosynthesis
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome P450 / heme enzyme / rufomycin / ligand-free
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces atratus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsWang, Y. / Jordan, S. / Li, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147510 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural and spectroscopic characterization of RufO indicates a new biological role in rufomycin biosynthesis.
Authors: Jordan, S. / Li, B. / Traore, E. / Wu, Y. / Usai, R. / Liu, A. / Xie, Z.R. / Wang, Y.
History
DepositionMay 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0592
Polymers43,4431
Non-polymers6161
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.686, 77.686, 137.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cytochrome P450


Mass: 43442.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces atratus (bacteria) / Gene: rufO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A224AU14
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium tartrate dibasic dihydrate and 20% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 33478 / % possible obs: 96.7 % / Redundancy: 19.8 % / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.036 / Rrim(I) all: 0.157 / Χ2: 1.04 / Net I/σ(I): 5.7 / Num. measured all: 664064
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.89-1.9217.30.93815520.9470.9860.2040.9620.67891.9
1.92-1.9618.61.05115870.9310.9820.2261.0770.65693.4
1.96-219.50.8716260.9490.9870.1840.890.63394.8
2-2.0420.30.7316000.9660.9910.1530.7470.65896.2
2.04-2.08210.63516150.9740.9930.1330.650.69295.7
2.08-2.1320.90.51816390.9850.9960.1080.530.72395.8
2.13-2.18200.45916320.9880.9970.0990.470.73995.6
2.18-2.2419.30.42616060.9880.9970.0940.4360.76394.1
2.24-2.3121.10.33716360.9880.9970.070.3441.00696.3
2.31-2.3822.50.27916630.9950.9990.0570.2850.82797
2.38-2.47220.25216670.9950.9990.0520.2570.85198
2.47-2.5721.40.20616960.9960.9990.0430.2110.91198.5
2.57-2.6820.90.19817160.9950.9990.0420.2030.96899.5
2.68-2.8220.50.17117170.9950.9990.0380.1751.06599.6
2.82-319.70.15417380.9950.9990.0360.1591.24799.5
3-3.23180.14616950.9910.9980.0370.1511.45397.8
3.23-3.5621.60.12317460.9960.9990.0290.1261.68799.7
3.56-4.0719.10.11417110.9940.9980.0290.1171.8997
4.07-5.1316.50.10217450.9910.9980.0280.1061.87496.7
5.13-5016.80.08118910.9960.9990.0220.0851.49497.5

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALEPACKdata scaling
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R9C

3r9c


Resolution: 1.89→42.87 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1997 5.99 %
Rwork0.1923 --
obs0.1948 33346 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 43 335 3233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062997
X-RAY DIFFRACTIONf_angle_d0.8364108
X-RAY DIFFRACTIONf_dihedral_angle_d13.4881100
X-RAY DIFFRACTIONf_chiral_restr0.048451
X-RAY DIFFRACTIONf_plane_restr0.009548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.930.40431310.32632043X-RAY DIFFRACTION90
1.93-1.990.31691360.26462147X-RAY DIFFRACTION94
1.99-2.040.31481400.23322189X-RAY DIFFRACTION95
2.04-2.110.27961390.20482174X-RAY DIFFRACTION96
2.11-2.190.25711370.20692159X-RAY DIFFRACTION95
2.19-2.270.25581400.2232178X-RAY DIFFRACTION94
2.27-2.380.23461410.20122223X-RAY DIFFRACTION97
2.38-2.50.2911440.2022259X-RAY DIFFRACTION98
2.5-2.660.27551440.20792271X-RAY DIFFRACTION99
2.66-2.860.24191470.2062306X-RAY DIFFRACTION100
2.86-3.150.27321480.21542307X-RAY DIFFRACTION99
3.15-3.610.22141480.18512332X-RAY DIFFRACTION99
3.61-4.550.19161470.162304X-RAY DIFFRACTION97
4.55-42.870.20361550.17342457X-RAY DIFFRACTION97

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