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- PDB-6m4p: Cytochrome P450 monooxygenase StvP2 substrate-bound structure -

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Basic information

Entry
Database: PDB / ID: 6m4p
TitleCytochrome P450 monooxygenase StvP2 substrate-bound structure
ComponentsCytochrome P450
KeywordsANTIBIOTIC / P450 Anti-MRSA Streptovaricin C Methylenedioxy Bridge StvP2 substrate-bound structure
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
6-methoxy-streptovaricin C / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces spectabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSun, G. / Hu, C. / Mei, Q. / Luo, M. / Chen, X. / Li, Z. / Liu, Y. / Deng, Z. / Zhang, Z. / Sun, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903200 China
National Natural Science Foundation of China (NSFC)31800052 China
CitationJournal: Nat Commun / Year: 2020
Title: Uncovering the cytochrome P450-catalyzed methylenedioxy bridge formation in streptovaricins biosynthesis.
Authors: Sun, G. / Hu, C. / Mei, Q. / Luo, M. / Chen, X. / Li, Z. / Liu, Y. / Deng, Z. / Zhang, Z. / Sun, Y.
History
DepositionMar 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4796
Polymers87,7032
Non-polymers2,7774
Water5,423301
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2403
Polymers43,8511
Non-polymers1,3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-26 kcal/mol
Surface area15690 Å2
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2403
Polymers43,8511
Non-polymers1,3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-26 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.638, 87.254, 78.789
Angle α, β, γ (deg.)90.000, 112.281, 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

#1: Protein Cytochrome P450


Mass: 43851.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces spectabilis (bacteria) / Gene: stvP2 / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A286SBY7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-F4O / 6-methoxy-streptovaricin C


Mass: 771.847 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H53NO14 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Salt: 0.17M Ammonium acetate Buffer: 0.085M Sodium citrate tribasic dihydrate pH5.6 Precipitant: 24%w/v polyethylene glycol 4000 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9879 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9879 Å / Relative weight: 1
ReflectionResolution: 2.3→19.78 Å / Num. obs: 34238 / % possible obs: 99.24 % / Redundancy: 6.5 % / Biso Wilson estimate: 36.06 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1197 / Rpim(I) all: 0.051 / Rrim(I) all: 0.1304 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.6053 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 3425 / CC1/2: 0.841 / CC star: 0.956 / Rpim(I) all: 0.2528 / Rrim(I) all: 0.657 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OQR

4oqr


Resolution: 2.3→19.78 Å / SU ML: 0.3326 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2691 1594 4.66 %
Rwork0.2216 32583 -
obs0.2238 34177 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5753 0 196 301 6250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00366114
X-RAY DIFFRACTIONf_angle_d0.90868361
X-RAY DIFFRACTIONf_chiral_restr0.0672913
X-RAY DIFFRACTIONf_plane_restr0.00781088
X-RAY DIFFRACTIONf_dihedral_angle_d21.2358942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.29531330.26033020X-RAY DIFFRACTION99.97
2.37-2.460.29721480.25672924X-RAY DIFFRACTION99.93
2.46-2.560.3281560.25962973X-RAY DIFFRACTION99.94
2.56-2.670.33341280.26442971X-RAY DIFFRACTION99.87
2.67-2.810.29861470.26592942X-RAY DIFFRACTION98.91
2.81-2.990.3862990.27092955X-RAY DIFFRACTION99.67
2.99-3.220.32551400.24712973X-RAY DIFFRACTION99.49
3.22-3.540.28661910.22972915X-RAY DIFFRACTION99.36
3.54-4.050.2381600.19662929X-RAY DIFFRACTION98.75
4.05-5.090.22751580.18362970X-RAY DIFFRACTION99.3
5.09-19.780.22331340.19563011X-RAY DIFFRACTION98.62
Refinement TLS params.Method: refined / Origin x: -15.3988174199 Å / Origin y: -23.6072669003 Å / Origin z: -14.1945579312 Å
111213212223313233
T0.269433255628 Å20.0267952315226 Å2-0.00279906914427 Å2-0.270225537916 Å20.0106581994617 Å2--0.250145638761 Å2
L0.543779446248 °20.331874674431 °2-0.00877008632752 °2-0.439547928505 °20.028572733776 °2--0.135999780009 °2
S0.0163006326001 Å °0.0107324253372 Å °-0.00784637691657 Å °-0.000723774852482 Å °0.00349206920946 Å °0.00444657954441 Å °0.00230868770065 Å °-0.0123583250356 Å °-0.0206025683032 Å °
Refinement TLS groupSelection details: all

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