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- PDB-6vxv: Crystal structure of cyclo-L-Trp-L-Pro-bound cytochrome P450 NasF... -

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Basic information

Entry
Database: PDB / ID: 6vxv
TitleCrystal structure of cyclo-L-Trp-L-Pro-bound cytochrome P450 NasF5053 from Streptomyces sp. NRRL F-5053
Componentscytochrome P450 NasF5053
KeywordsOXIDOREDUCTASE / biosynthetic protein / cytochrome P450 / cyclodipeptide / regio-selecitivty / stereo-selectivity / pyrroloindoline alkaloids / radical mediated reaction / F5053 / Streptomyces
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / Chem-QRP
Function and homology information
Biological speciesStreptomyces sp. NRRL F-5053 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLuo, Z. / Jia, X. / Sun, C. / Qu, X. / Kobe, B.
Funding support Australia, China, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Natural Science Foundation of China (NSFC)31770063 China
CitationJournal: Nat Commun / Year: 2020
Title: Molecular basis of regio- and stereo-specificity in biosynthesis of bacterial heterodimeric diketopiperazines.
Authors: Sun, C. / Luo, Z. / Zhang, W. / Tian, W. / Peng, H. / Lin, Z. / Deng, Z. / Kobe, B. / Jia, X. / Qu, X.
History
DepositionFeb 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytochrome P450 NasF5053
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7056
Polymers43,4591
Non-polymers1,2465
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-42 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.314, 91.836, 93.604
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-832-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein cytochrome P450 NasF5053


Mass: 43459.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NRRL F-5053 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 5 types, 356 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-QRP / (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione / Brevianamide F / cyclo-L-Trp-L-Pro


Mass: 283.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17N3O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal*YM
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M calcium chloride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.6→46.8 Å / Num. obs: 48951 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.96 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Χ2: 0.96 / Net I/σ(I): 11.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.177 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2415 / CC1/2: 0.709 / Rpim(I) all: 0.476 / Rrim(I) all: 1.271 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ABB

3abb


Resolution: 1.6→46.8 Å / SU ML: 0.1716 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0621 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 2431 4.97 %Random selection of 5% diffraction data
Rwork0.1696 46446 --
obs0.1712 48877 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 87 351 3476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523241
X-RAY DIFFRACTIONf_angle_d0.93114428
X-RAY DIFFRACTIONf_chiral_restr0.0535476
X-RAY DIFFRACTIONf_plane_restr0.0048582
X-RAY DIFFRACTIONf_dihedral_angle_d16.04691913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.30471510.28662681X-RAY DIFFRACTION99.54
1.63-1.670.30981290.27152667X-RAY DIFFRACTION99.36
1.67-1.710.25581540.2482689X-RAY DIFFRACTION99.41
1.71-1.750.2741600.23742655X-RAY DIFFRACTION99.75
1.75-1.80.29321330.21452722X-RAY DIFFRACTION99.65
1.8-1.850.22361510.19672677X-RAY DIFFRACTION99.68
1.85-1.910.21931580.17762700X-RAY DIFFRACTION99.86
1.91-1.980.25231180.17452721X-RAY DIFFRACTION99.89
1.98-2.060.24341260.17262719X-RAY DIFFRACTION99.58
2.06-2.150.21421420.16652735X-RAY DIFFRACTION99.72
2.15-2.260.20171410.15532717X-RAY DIFFRACTION99.86
2.26-2.410.22271550.16422721X-RAY DIFFRACTION99.83
2.41-2.590.19221340.16782744X-RAY DIFFRACTION99.83
2.59-2.850.20511480.1722766X-RAY DIFFRACTION99.97
2.85-3.270.17551520.16832764X-RAY DIFFRACTION99.9
3.27-4.110.16551380.14032806X-RAY DIFFRACTION99.97
4.11-46.80.18281410.15612962X-RAY DIFFRACTION99.71

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