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- PDB-3wvs: Crystal Structure of Cytochrome P450revI -

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Basic information

Entry
Database: PDB / ID: 3wvs
TitleCrystal Structure of Cytochrome P450revI
ComponentsPutative monooxygenase
KeywordsOXIDOREDUCTASE / Monooxygenase
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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-RRM / L(+)-TARTARIC ACID / Putative monooxygenase
Similarity search - Component
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsNagano, S. / Takahashi, S. / Osada, H. / Shiro, Y.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure-function analyses of cytochrome P450revI involved in reveromycin A biosynthesis and evaluation of the biological activity of its substrate, reveromycin T.
Authors: Takahashi, S. / Nagano, S. / Nogawa, T. / Kanoh, N. / Uramoto, M. / Kawatani, M. / Shimizu, T. / Miyazawa, T. / Shiro, Y. / Osada, H.
History
DepositionJun 6, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5249
Polymers44,7521
Non-polymers1,7728
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.779, 73.472, 58.305
Angle α, β, γ (deg.)90.000, 112.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative monooxygenase / Cytochrome P450revI


Mass: 44751.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Strain: SN-593 / Gene: revI / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: G1UDU7

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Non-polymers , 5 types, 399 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-RRM / (2E,4S,5S,6E,8E)-10-{(2R,3S,6S,8R,9S)-9-butyl-8-[(1E,3E)-4-carboxy-3-methylbuta-1,3-dien-1-yl]-3-methyl-1,7-dioxaspiro[5.5]undec-2-yl}-5-hydroxy-4,8-dimethyldeca-2,6,8-trienoic acid


Mass: 544.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H48O7
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG3350, Tartrate, pH 7.5, vapor diffusion, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL40B210.93
SYNCHROTRONSPring-8 BL44B221.73819, 1.74069, 1.71660
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 10, 2008
ADSC QUANTUM 2102CCDApr 18, 2008
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHx-ray1
2Si 111 CHANNELMADx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.931
21.738191
31.740691
41.71661
ReflectionResolution: 1.35→50 Å / Num. all: 81049 / Num. obs: 81049 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.4→1.4 Å / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefmac_5.4.0077refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.4→27.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.171 / SU B: 0.823 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 4061 5 %RANDOM
Rwork0.1732 ---
all0.174 81016 --
obs0.174 81016 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 43.11 Å2 / Biso mean: 11.792 Å2 / Biso min: 3.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20.27 Å2
2---0.42 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 122 391 3603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223390
X-RAY DIFFRACTIONr_angle_refined_deg1.1612.0444623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9335418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.65122.517151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93915553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5191537
X-RAY DIFFRACTIONr_chiral_restr0.0690.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212623
X-RAY DIFFRACTIONr_mcbond_it0.4361.52038
X-RAY DIFFRACTIONr_mcangle_it0.86623289
X-RAY DIFFRACTIONr_scbond_it1.4231352
X-RAY DIFFRACTIONr_scangle_it2.3354.51330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.399-1.4360.2663020.2285536601597.057
1.436-1.4750.2132670.2025552582099.983
1.475-1.5180.2132650.1925407567499.965
1.518-1.5640.2122670.1875264553299.982
1.564-1.6150.1792580.1815082534199.981
1.615-1.6720.1892850.1754875516299.961
1.672-1.7350.1912320.1794741497799.92
1.735-1.8060.2172380.174560479999.979
1.806-1.8860.1962190.17244284647100
1.886-1.9780.1842410.1714106435199.908
1.978-2.0850.1872320.1713993422899.929
2.085-2.2110.1781950.16937613956100
2.211-2.3640.1792110.1733513372699.946
2.364-2.5530.2021810.1663295347899.942
2.553-2.7960.1941580.1723061322199.938
2.796-3.1250.1971570.172749291199.828
3.125-3.6060.1481060.1572454256399.883
3.606-4.4110.1391090.1452062217799.724
4.411-6.2180.179840.1721616170299.882
6.218-53.9950.226540.20890096998.452

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