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- PDB-5z9i: Identification of the functions of unusual cytochrome p450-like m... -

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Basic information

Entry
Database: PDB / ID: 5z9i
TitleIdentification of the functions of unusual cytochrome p450-like monooxygenases involved in microbial secondary metablism
ComponentsPutative P450-like enzyme
KeywordsOXIDOREDUCTASE / cytochrome p450 / 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 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Putative P450-like enzyme
Similarity search - Component
Biological speciesStreptomyces himastatinicus ATCC 53653 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsLu, M. / Lin, L. / Zhang, C. / Chen, Y.
CitationJournal: Chembiochem / Year: 2020
Title: Riboflavin Is Directly Involved in the N-Dealkylation Catalyzed by Bacterial Cytochrome P450 Monooxygenases.
Authors: Zhang, C. / Lu, M. / Lin, L. / Huang, Z. / Zhang, R. / Wu, X. / Chen, Y.
History
DepositionFeb 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Putative P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3862
Polymers44,7701
Non-polymers6161
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.987, 72.492, 98.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative P450-like enzyme


Mass: 44769.738 Da / Num. of mol.: 1 / Mutation: L340F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces himastatinicus ATCC 53653 (bacteria)
Gene: hmtS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G0LWB2
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Bis-Tris hydrochloride, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 2.2→45.282 Å / Num. obs: 40569 / % possible obs: 99.1 % / Redundancy: 3.442 % / Biso Wilson estimate: 36.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.077 / Χ2: 1.03 / Net I/σ(I): 13.17 / Num. measured all: 139630
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.333.2140.442.8820699663564400.8260.52697.1
2.33-2.493.5120.3314.1921659618461680.9080.3999.7
2.49-2.693.530.2086.2620297576957500.9570.24599.7
2.69-2.953.3910.1338.9218046533553210.980.15799.7
2.95-3.293.580.08513.917238483348150.9910.199.6
3.29-3.83.3840.05121.414263424342150.9960.0699.3
3.8-4.653.5730.03830.3812756358035700.9970.04599.7
4.65-6.543.4110.03630.369408278127580.9970.04399.2
6.54-45.2823.4360.02837.345264155715320.9980.03498.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.199→45.282 Å / FOM work R set: 0.8494 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.72 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2336 3715 9.16 %
Rwork0.1831 36853 -
obs0.1877 40568 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.67 Å2 / Biso mean: 47.32 Å2 / Biso min: 19.77 Å2
Refinement stepCycle: final / Resolution: 2.199→45.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 43 113 3067
Biso mean--20 43.76 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093041
X-RAY DIFFRACTIONf_angle_d1.4714159
X-RAY DIFFRACTIONf_chiral_restr0.046464
X-RAY DIFFRACTIONf_plane_restr0.006544
X-RAY DIFFRACTIONf_dihedral_angle_d13.4541083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1989-2.22680.28541250.23971240136590
2.2268-2.25610.31391360.23651352148899
2.2561-2.2870.30651390.24071365150499
2.287-2.31960.2791380.234513751513100
2.3196-2.35430.28791410.231213661507100
2.3543-2.39110.28991370.22441362149999
2.3911-2.43030.28961450.220113801525100
2.4303-2.47220.29011360.218813631499100
2.4722-2.51710.30971330.204814021535100
2.5171-2.56550.27191410.20713591500100
2.5655-2.61790.2341370.200113691506100
2.6179-2.67480.23411410.206813791520100
2.6748-2.7370.26851420.201313881530100
2.737-2.80540.25121290.18871345147499
2.8054-2.88130.21271370.181913901527100
2.8813-2.96610.24421380.189513731511100
2.9661-3.06180.2641410.184613751516100
3.0618-3.17120.28321340.198113751509100
3.1712-3.29810.23761380.182813741512100
3.2981-3.44820.21431380.177513691507100
3.4482-3.62990.24361400.1641372151299
3.6299-3.85720.20651360.16351355149199
3.8572-4.15480.1471380.15613531491100
4.1548-4.57260.20541360.151214001536100
4.5726-5.23340.23521370.16491368150599
5.2334-6.59030.26231400.21061350149099
6.5903-45.29180.19981420.1631354149698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2760.9785-0.10082.86570.5983.00390.3502-0.45330.19351.0344-0.414-0.0073-0.0206-0.41060.06720.6467-0.0827-0.01540.476-0.01460.2866-20.6587-12.729932.1109
21.5260.23880.08882.53770.64742.3211-0.02080.15660.0402-0.09250.0727-0.0598-0.1628-0.1092-0.05770.15150.034-0.00870.27350.00410.2403-11.3356-8.74267.6354
35.21330.2565-0.45624.0359-0.19982.7066-0.2266-0.13730.63650.19770.25260.0431-0.035-0.2178-0.03760.24510.0408-0.08230.4072-0.03910.3449-23.6385-13.67665.1513
41.75991.21360.44253.37020.53050.84760.153-0.2910.07040.6751-0.1583-0.385-0.0949-0.06130.03570.35640.0188-0.10610.3085-0.02020.3314-9.1451-5.217323.661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 67 )A7 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 149 )A68 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 223 )A150 - 223
4X-RAY DIFFRACTION4chain 'A' and (resid 224 through 398 )A224 - 398

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