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- PDB-5l1r: X-ray Structure of the Substrate-free Cytochrome P450 PntM -

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Basic information

Entry
Database: PDB / ID: 5l1r
TitleX-ray Structure of the Substrate-free Cytochrome P450 PntM
ComponentsPentalenolactone synthase
KeywordsOXIDOREDUCTASE / PntM / cytochrome P450 / bicine
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
PROTOPORPHYRIN IX CONTAINING FE / Pentalenolactone synthase
Similarity search - Component
Biological speciesStreptomyces arenae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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)45,2843
Polymers44,5051
Non-polymers7802
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.456, 164.588, 82.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 3.41 Å3/Da / Density % sol: 63.98 % / Mosaicity: 0.15 °
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→45.65 Å / Num. obs: 41488 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 20.2 / Num. measured all: 285368 / Scaling rejects: 467
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.054.60.2470.935190.9
8.94-45.656.10.030.999199.6

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIXdev_2474refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x9p

2x9p


Resolution: 2→45.65 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.96
RfactorNum. reflection% reflection
Rfree0.1727 2128 5.14 %
Rwork0.1442 --
obs0.1458 41435 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.45 Å2 / Biso mean: 20.342 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 2→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 54 619 3774
Biso mean--16.4 34.55 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073241
X-RAY DIFFRACTIONf_angle_d0.9224417
X-RAY DIFFRACTIONf_chiral_restr0.051490
X-RAY DIFFRACTIONf_plane_restr0.005585
X-RAY DIFFRACTIONf_dihedral_angle_d6.3372705
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 (%)
2-2.04650.22431240.17642329245390
2.0465-2.09770.20531160.15712532264897
2.0977-2.15440.18851690.145425712740100
2.1544-2.21780.20211220.14526472769100
2.2178-2.28940.17691330.145125872720100
2.2894-2.37120.18891320.147126342766100
2.3712-2.46620.16491280.144626452773100
2.4662-2.57840.20791610.152825882749100
2.5784-2.71430.18411530.157525882741100
2.7143-2.88440.1691450.154226492794100
2.8844-3.1070.18621490.157926412790100
3.107-3.41960.18541290.137426842813100
3.4196-3.91420.13691540.122626562810100
3.9142-4.93050.13111490.117727232872100
4.9305-45.66140.17251640.159428332997100
Refinement TLS params.Method: refined / Origin x: 20.7892 Å / Origin y: 27.0466 Å / Origin z: 20.3701 Å
111213212223313233
T0.0593 Å2-0.0082 Å2-0.0113 Å2-0.0785 Å2-0.0059 Å2--0.0817 Å2
L0.7924 °20.0418 °2-0.1492 °2-0.851 °2-0.2315 °2--0.8431 °2
S-0.0205 Å °-0.0338 Å °-0.0772 Å °0.0095 Å °-0.0109 Å °-0.0402 Å °0.056 Å °0.0009 Å °0.0211 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 - 619

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