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- PDB-5l1v: X-ray Structure of M81C mutant of Cytochrome P450 PntM with penta... -

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Basic information

Entry
Database: PDB / ID: 5l1v
TitleX-ray Structure of M81C mutant of Cytochrome P450 PntM with pentalenolactone F
ComponentsPentalenolactone synthase
KeywordsOXIDOREDUCTASE / PntM / cytochrome P450 / pentalenolactone F / mutant / M81C
Function / homology
Function and homology information


pentalenolactone synthase / pentalenolactone biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / 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
pentalenolactone F / PROTOPORPHYRIN IX CONTAINING FE / Pentalenolactone synthase
Similarity search - Component
Biological speciesStreptomyces arenae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsDuan, L. / Jogl, G. / Cane, D.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: The Cytochrome P450-Catalyzed Oxidative Rearrangement in the Final Step of Pentalenolactone Biosynthesis: Substrate Structure Determines Mechanism.
Authors: Duan, L. / Jogl, G. / Cane, D.E.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pentalenolactone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3723
Polymers44,4771
Non-polymers8952
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.563, 164.234, 82.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-666-

HOH

21A-1028-

HOH

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Components

#1: Protein Pentalenolactone synthase / Pentalenolactone biosynthesis protein M


Mass: 44476.758 Da / Num. of mol.: 1 / Mutation: M81C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces arenae (bacteria) / Strain: Tu469 / Gene: pntM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3VWI3, pentalenolactone synthase
#2: Chemical ChemComp-7PF / pentalenolactone F / (2R,4a'R,7a'S,9a'R)-6',6'-dimethyl-3'-oxo-1',5',6',7',7a',9a'-hexahydro-3'H-spiro[oxirane-2,4'-pentaleno[1,6a-c]pyran]-9'-carboxylic acid


Mass: 278.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18O5
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 3.45 Å3/Da / Density % sol: 64.3 % / Mosaicity: 0.29 °
Crystal growTemperature: 288 K / Method: evaporation / pH: 9 / Details: Bicine, sodium citrate, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 31, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.12→45.69 Å / Num. obs: 35534 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 17.38 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.255 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.12-2.187.10.9980.7021100
8.99-45.696.20.0510.998199.6

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIXdev_2463refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x9p

2x9p


Resolution: 2.12→45.69 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.91
RfactorNum. reflection% reflection
Rfree0.1953 1836 5.17 %
Rwork0.1604 --
obs0.1623 35479 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.01 Å2 / Biso mean: 22.9533 Å2 / Biso min: 7.33 Å2
Refinement stepCycle: final / Resolution: 2.12→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 63 551 3713
Biso mean--15.11 35.3 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083256
X-RAY DIFFRACTIONf_angle_d0.974448
X-RAY DIFFRACTIONf_chiral_restr0.052494
X-RAY DIFFRACTIONf_plane_restr0.006587
X-RAY DIFFRACTIONf_dihedral_angle_d11.5771255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.12-2.17740.2661460.22925112657
2.1774-2.24140.24531320.209525812713
2.2414-2.31380.2851200.201325312651
2.3138-2.39650.23191320.188925532685
2.3965-2.49240.23991280.178826002728
2.4924-2.60580.23131660.173125082674
2.6058-2.74320.20861420.176725602702
2.7432-2.9150.23981400.167925732713
2.915-3.14010.18681490.160825762725
3.1401-3.4560.18121210.14126192740
3.456-3.95580.16131570.123726012758
3.9558-4.98290.12611410.119526512792
4.9829-45.70490.17691620.162527792941
Refinement TLS params.Method: refined / Origin x: 20.9601 Å / Origin y: 26.9784 Å / Origin z: 20.3972 Å
111213212223313233
T0.0885 Å2-0.0058 Å2-0.011 Å2-0.0952 Å2-0.0051 Å2--0.0973 Å2
L0.7099 °20.0563 °2-0.0913 °2-0.8001 °2-0.1951 °2--0.7487 °2
S-0.0122 Å °-0.0247 Å °-0.049 Å °0.0042 Å °-0.0039 Å °-0.0416 Å °0.0478 Å °-0.0015 Å °0.0125 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allX1
2X-RAY DIFFRACTION1allY501
3X-RAY DIFFRACTION1allA2 - 398
4X-RAY DIFFRACTION1allS1 - 560

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