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- PDB-5l1u: X-ray Structure of M81A mutant of Cytochrome P450 PntM with penta... -

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Basic information

Entry
Database: PDB / ID: 5l1u
TitleX-ray Structure of M81A mutant of Cytochrome P450 PntM with pentalenolactone F
ComponentsPentalenolactone synthase
KeywordsOXIDOREDUCTASE / PntM / cytochrome P450 / pentalenolactone F / mutant / M81A
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: 2.074 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)45,3393
Polymers44,4451
Non-polymers8952
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.623, 163.860, 82.217
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-671-

HOH

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Components

#1: Protein Pentalenolactone synthase / Pentalenolactone biosynthesis protein M


Mass: 44444.691 Da / Num. of mol.: 1 / Mutation: M81A
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.: 491 / 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: 63.96 % / Mosaicity: 0.19 °
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: 2.07→45.5 Å / Num. obs: 37040 / % possible obs: 98.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 14.71 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.139 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.07-2.134.70.4560.809191.3
9.04-45.56.10.0420.999199.6

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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: 2.074→45.495 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17
RfactorNum. reflection% reflection
Rfree0.1844 1913 5.17 %
Rwork0.1542 --
obs0.1558 36998 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.01 Å2 / Biso mean: 19.4115 Å2 / Biso min: 5.33 Å2
Refinement stepCycle: final / Resolution: 2.074→45.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 63 491 3652
Biso mean--10.9 30.7 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083286
X-RAY DIFFRACTIONf_angle_d0.9724493
X-RAY DIFFRACTIONf_chiral_restr0.052498
X-RAY DIFFRACTIONf_plane_restr0.006595
X-RAY DIFFRACTIONf_dihedral_angle_d9.1481268
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 (%)
2.0737-2.12550.24511330.20692280241390
2.1255-2.1830.24371260.17424632589100
2.183-2.24720.18191240.16742446257097
2.2472-2.31980.21741260.161424802606100
2.3198-2.40270.19891310.15892448257998
2.4027-2.49890.20331250.15342497262298
2.4989-2.61260.21321520.15424952647100
2.6126-2.75030.16761430.16252501264499
2.7503-2.92260.21371340.15992490262499
2.9226-3.14820.17181490.158825292678100
3.1482-3.46490.18771190.143725702689100
3.4649-3.9660.17111530.13125292682100
3.966-4.99580.12641410.126526182759100
4.9958-45.50630.18431570.171627392896100
Refinement TLS params.Method: refined / Origin x: 21.0267 Å / Origin y: 26.8583 Å / Origin z: 20.2265 Å
111213212223313233
T0.0584 Å2-0.0063 Å2-0.0089 Å2-0.0705 Å2-0.0056 Å2--0.0709 Å2
L0.7622 °20.049 °2-0.0897 °2-0.8551 °2-0.1289 °2--0.8321 °2
S-0.0131 Å °-0.0427 Å °-0.0632 Å °0.0056 Å °-0.0053 Å °-0.0295 Å °0.0261 Å °-0.0088 Å °0.0144 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 - 491

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