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- PDB-5l1w: X-ray Structure of 2-Mercaptoethanol modified M81C mutant of Cyto... -

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Basic information

Entry
Database: PDB / ID: 5l1w
TitleX-ray Structure of 2-Mercaptoethanol modified M81C mutant of Cytochrome P450 PntM with pentalenolactone F
ComponentsPentalenolactone synthase
KeywordsOXIDOREDUCTASE / PntM / cytochrome P450 / pentalenolactone F / mutant / M81C / 2-Mercaptoethanol
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: 2.06 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)45,4483
Polymers44,5531
Non-polymers8952
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.574, 163.227, 83.289
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-514-

HOH

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Components

#1: Protein Pentalenolactone synthase / Pentalenolactone biosynthesis protein M


Mass: 44552.875 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.: 631 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.43 Å3/Da / Density % sol: 64.16 % / Mosaicity: 0.22 °
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: 2.06→44.57 Å / Num. obs: 37442 / % possible obs: 97.2 % / Redundancy: 7.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.134 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.06-2.126.50.4590.821192
8.98-44.576.20.030.998199.5

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHENIX1.10pre_2131refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x9p

2x9p


Resolution: 2.06→43 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.18
RfactorNum. reflection% reflection
Rfree0.1864 1916 5.12 %
Rwork0.1611 --
obs0.1624 37401 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.49 Å2 / Biso mean: 18.8447 Å2 / Biso min: 3.81 Å2
Refinement stepCycle: final / Resolution: 2.06→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 63 631 3797
Biso mean--10.62 31.61 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053266
X-RAY DIFFRACTIONf_angle_d0.8744461
X-RAY DIFFRACTIONf_chiral_restr0.048495
X-RAY DIFFRACTIONf_plane_restr0.005588
X-RAY DIFFRACTIONf_dihedral_angle_d16.3292019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.06-2.11150.22281060.19682348245491
2.1115-2.16860.2291520.19122419257196
2.1686-2.23240.22711240.18772462258695
2.2324-2.30450.24581230.18382504262797
2.3045-2.38680.20821290.17552501263097
2.3868-2.48240.23341260.17152485261195
2.4824-2.59530.21821540.16762495264998
2.5953-2.73220.1571400.16822532267298
2.7322-2.90330.19021410.16322544268598
2.9033-3.12740.1981440.16622547269198
3.1274-3.4420.18971170.15342587270498
3.442-3.93980.15521530.13822607276099
3.9398-4.96250.13121450.12782667281299
4.9625-43.00890.18041620.162427872949100
Refinement TLS params.Method: refined / Origin x: 21.1722 Å / Origin y: 26.6962 Å / Origin z: 20.3464 Å
111213212223313233
T0.0389 Å2-0.0011 Å2-0.0072 Å2-0.0452 Å20.0101 Å2--0.0573 Å2
L0.3678 °20.1025 °2-0.0141 °2-0.3767 °2-0.0179 °2--0.4169 °2
S-0.0148 Å °-0.024 Å °-0.0422 Å °0.0056 Å °-0.0103 Å °-0.0344 Å °0.0026 Å °-0.0149 Å °-0.0107 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 - 631

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