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- PDB-6vzb: Crystal structure of cytochrome P450 NasF5053 S284A-V288A mutant ... -

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Basic information

Entry
Database: PDB / ID: 6vzb
TitleCrystal structure of cytochrome P450 NasF5053 S284A-V288A mutant variant from Streptomyces sp. NRRL F-5053 in the cyclo-L-Trp-L-Pro-bound state
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: 1.68 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 28, 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)44,6215
Polymers43,4151
Non-polymers1,2064
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-36 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.236, 91.208, 93.460
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-826-

HOH

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Components

#1: Protein cytochrome P450 NasF5053


Mass: 43415.023 Da / Num. of mol.: 1 / Mutation: S284A,V288A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NRRL F-5053 (bacteria)
Production host: Escherichia coli (E. coli)
#2: 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293 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 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.68→46.73 Å / Num. obs: 41405 / % possible obs: 98.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.049 / Rrim(I) all: 0.128 / Χ2: 0.99 / Net I/σ(I): 12.1
Reflection shellResolution: 1.68→1.71 Å / Rmerge(I) obs: 1.041 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2011 / CC1/2: 0.744 / Rpim(I) all: 0.429 / Rrim(I) all: 1.128 / Χ2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX1.14_3260model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6VXV

6vxv


Resolution: 1.68→46.73 Å / SU ML: 0.1796 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3439 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2032 1974 4.77 %
Rwork0.1691 39389 -
obs0.1708 41363 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.56 Å2
Refinement stepCycle: LAST / Resolution: 1.68→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 86 342 3445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01023208
X-RAY DIFFRACTIONf_angle_d1.2074382
X-RAY DIFFRACTIONf_chiral_restr0.0582473
X-RAY DIFFRACTIONf_plane_restr0.0076574
X-RAY DIFFRACTIONf_dihedral_angle_d23.96781152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.33951240.25672672X-RAY DIFFRACTION94.81
1.72-1.770.24841420.22372784X-RAY DIFFRACTION97.5
1.77-1.820.27951220.20172738X-RAY DIFFRACTION97.44
1.82-1.880.21241240.18862778X-RAY DIFFRACTION97.68
1.88-1.940.2281600.17682757X-RAY DIFFRACTION97.79
1.94-2.020.25291500.17112788X-RAY DIFFRACTION98
2.02-2.110.21181550.1652775X-RAY DIFFRACTION98.06
2.11-2.230.2061120.1552825X-RAY DIFFRACTION98.26
2.23-2.360.19691370.15432809X-RAY DIFFRACTION98.73
2.36-2.550.19711740.15162773X-RAY DIFFRACTION98.36
2.55-2.80.19391350.15782865X-RAY DIFFRACTION98.85
2.8-3.210.1697980.16692902X-RAY DIFFRACTION98.68
3.21-4.040.18141510.14942904X-RAY DIFFRACTION99.29
4.04-46.730.191900.17893019X-RAY DIFFRACTION99.01

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