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- PDB-5l1q: X-ray Structure of Cytochrome P450 PntM with Dihydropentalenolactone F -

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Basic information

Entry
Database: PDB / ID: 5l1q
TitleX-ray Structure of Cytochrome P450 PntM with Dihydropentalenolactone F
ComponentsPentalenolactone synthase
KeywordsOXIDOREDUCTASE / PntM / cytochrome P450 / dihydropentalenolactone F
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
Dihydropentalenolactone F / PROTOPORPHYRIN IX CONTAINING FE / Pentalenolactone synthase
Similarity search - Component
Biological speciesStreptomyces arenae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 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)45,4023
Polymers44,5051
Non-polymers8972
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.527, 164.365, 82.044
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-603-

HOH

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Components

#1: Protein Pentalenolactone synthase / Pentalenolactone biosynthesis protein M


Mass: 44504.809 Da / Num. of mol.: 1
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-7DF / Dihydropentalenolactone F / (2R,4a'R,7a'R,9'R,9a'S)-6',6'-dimethyl-3'-oxooctahydro-3'H-spiro[oxirane-2,4'-pentaleno[1,6a-c]pyran]-9'-carboxylic acid


Mass: 280.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H20O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 3.4 Å3/Da / Density % sol: 63.87 % / Mosaicity: 0.28 °
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: 2.03→45.56 Å / Num. obs: 39835 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.97 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.079 / Rrim(I) all: 0.212 / Net I/σ(I): 8.7 / Num. measured all: 276720 / Scaling rejects: 211
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.03-2.0850.820.624197.2
9.08-45.566.10.0490.998199.6

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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: 2.03→45.56 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7
RfactorNum. reflection% reflection
Rfree0.19 2058 5.17 %
Rwork0.1599 --
obs0.1615 39783 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.49 Å2 / Biso mean: 22.4845 Å2 / Biso min: 7.69 Å2
Refinement stepCycle: final / Resolution: 2.03→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 63 481 3645
Biso mean--13.78 35.01 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083256
X-RAY DIFFRACTIONf_angle_d0.934448
X-RAY DIFFRACTIONf_chiral_restr0.051496
X-RAY DIFFRACTIONf_plane_restr0.005586
X-RAY DIFFRACTIONf_dihedral_angle_d10.6381255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0301-2.07730.2821260.23652386251296
2.0773-2.12930.25671480.205724732621100
2.1293-2.18680.2521250.196224552580100
2.1868-2.25120.23031270.184525092636100
2.2512-2.32390.22571260.178225022628100
2.3239-2.40690.22711310.168324752606100
2.4069-2.50330.18711290.160225042633100
2.5033-2.61720.22461530.164125102663100
2.6172-2.75520.19451450.16424882633100
2.7552-2.92770.21931340.158725022636100
2.9277-3.15370.17311490.158125312680100
3.1537-3.4710.19071190.139925442663100
3.471-3.9730.15341500.131525252675100
3.973-5.00460.13161390.125425952734100
5.0046-45.57440.17221570.172627262883100
Refinement TLS params.Method: refined / Origin x: 20.9148 Å / Origin y: 26.904 Å / Origin z: 20.1892 Å
111213212223313233
T0.088 Å2-0.0056 Å2-0.0109 Å2-0.0991 Å2-0.0024 Å2--0.0964 Å2
L0.6155 °20.0516 °2-0.0734 °2-0.8107 °2-0.1319 °2--0.6958 °2
S-0.0135 Å °-0.0147 Å °-0.0323 Å °0.0094 Å °-0.0061 Å °-0.018 Å °0.0328 Å °-0.0183 Å °0.0153 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allY501
2X-RAY DIFFRACTION1allA2 - 398
3X-RAY DIFFRACTION1allX601
4X-RAY DIFFRACTION1allS1 - 481

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