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- PDB-6w0s: Crystal structure of substrate free cytochrome P450 NasF5053 from... -

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Basic information

Entry
Database: PDB / ID: 6w0s
TitleCrystal structure of substrate free cytochrome P450 NasF5053 from Streptomyces sp. NRRL F-5053
Componentscytochrome P450-F5053
KeywordsOXIDOREDUCTASE / biosynthetic protein / cytochrome P450 / cyclodipeptide / regio-selecitivty / stereo-selectivity / pyrroloindoline alkaloids / radical mediated reaction / F5053 / Streptomyces
Function / homologyBROMIDE ION / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesStreptomyces sp. NRRL F-5053 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionMar 2, 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

Downloads & links

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Assembly

Deposited unit
A: cytochrome P450-F5053
B: cytochrome P450-F5053
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,82217
Polymers86,9182
Non-polymers1,90315
Water13,475748
1
A: cytochrome P450-F5053
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,49210
Polymers43,4591
Non-polymers1,0339
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cytochrome P450-F5053
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3297
Polymers43,4591
Non-polymers8706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.208, 91.325, 98.275
Angle α, β, γ (deg.)90.000, 96.407, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein cytochrome P450-F5053


Mass: 43459.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NRRL F-5053 (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 763 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
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: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.7→45.66 Å / Num. obs: 81192 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.48 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Χ2: 0.97 / Net I/σ(I): 9
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2 / Num. unique obs: 4234 / CC1/2: 0.789 / Rpim(I) all: 0.392 / Rrim(I) all: 0.942 / Χ2: 1.04

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Processing

Software
NameVersionClassification
PHENIX1.14_3260model building
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WP2

5wp2


Resolution: 1.7→43.06 Å / SU ML: 0.1794 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4871
RfactorNum. reflection% reflection
Rfree0.2202 4133 5.1 %
Rwork0.1857 --
obs0.1874 81067 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 104 748 6952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01636381
X-RAY DIFFRACTIONf_angle_d1.40628707
X-RAY DIFFRACTIONf_chiral_restr0.0708943
X-RAY DIFFRACTIONf_plane_restr0.00911151
X-RAY DIFFRACTIONf_dihedral_angle_d22.29123741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.26661410.26972507X-RAY DIFFRACTION98.62
1.72-1.740.30751350.2612548X-RAY DIFFRACTION99.44
1.74-1.760.23691260.24772577X-RAY DIFFRACTION99.27
1.76-1.780.30231320.23392511X-RAY DIFFRACTION98.91
1.78-1.810.23391660.21982502X-RAY DIFFRACTION99.4
1.81-1.830.221580.20252579X-RAY DIFFRACTION99.64
1.83-1.860.23791310.20022546X-RAY DIFFRACTION99.78
1.86-1.890.24331320.20122572X-RAY DIFFRACTION99.89
1.89-1.910.26151460.19982558X-RAY DIFFRACTION99.71
1.91-1.950.24121180.19782550X-RAY DIFFRACTION99.96
1.95-1.980.23511410.19682580X-RAY DIFFRACTION99.89
1.98-2.020.23721530.18242557X-RAY DIFFRACTION99.74
2.02-2.050.2381270.17822571X-RAY DIFFRACTION99.74
2.05-2.10.20791350.17942560X-RAY DIFFRACTION99.67
2.1-2.140.23131370.17442545X-RAY DIFFRACTION99.67
2.14-2.190.2421350.17152552X-RAY DIFFRACTION99.74
2.19-2.250.19181460.16592559X-RAY DIFFRACTION99.74
2.25-2.310.27141210.1722586X-RAY DIFFRACTION99.93
2.31-2.380.22721440.16962557X-RAY DIFFRACTION99.78
2.38-2.450.17251570.16352561X-RAY DIFFRACTION99.74
2.45-2.540.1931360.16692551X-RAY DIFFRACTION99.89
2.54-2.640.23071400.17612615X-RAY DIFFRACTION99.82
2.64-2.760.20711440.17482526X-RAY DIFFRACTION99.85
2.76-2.910.18791360.18192560X-RAY DIFFRACTION99.89
2.91-3.090.21491420.18612580X-RAY DIFFRACTION99.74
3.09-3.330.23891170.18282601X-RAY DIFFRACTION99.89
3.33-3.660.17541420.18072567X-RAY DIFFRACTION99.85
3.66-4.190.21721330.17012621X-RAY DIFFRACTION99.89
4.19-5.280.19121310.1732614X-RAY DIFFRACTION99.71
5.28-43.060.26711310.22112621X-RAY DIFFRACTION99.14

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