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- PDB-7dvo: Structure of Reaction Intermediate of Cytochrome P450 NO Reductas... -

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Basic information

Entry
Database: PDB / ID: 7dvo
TitleStructure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL
ComponentsNADP nitrous oxide-forming nitric oxide reductase
KeywordsOXIDOREDUCTASE / heme enzyme / METAL BINDING PROTEIN
Function / homology
Function and homology information


nitric oxide reductase [NAD(P)+, nitrous oxide-forming] / nitric oxide reductase [NAD(P)H] activity / 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
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / NADP nitrous oxide-forming nitric oxide reductase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Model detailscytochrome P450nor
AuthorsNomura, T. / Kimura, T. / Kanematsu, Y. / Yamashita, K. / Hirata, K. / Ueno, G. / Murakami, H. / Hisano, T. / Yamagiwa, R. / Takeda, H. ...Nomura, T. / Kimura, T. / Kanematsu, Y. / Yamashita, K. / Hirata, K. / Ueno, G. / Murakami, H. / Hisano, T. / Yamagiwa, R. / Takeda, H. / Gopalasingam, C. / Yuki, K. / Kousaka, R. / Yanagasawa, S. / Shoji, O. / Kumasaka, T. / Takano, Y. / Ago, H. / Yamamoto, M. / Sugimoto, H. / Tosha, T. / Kubo, M. / Shiro, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05784 Japan
Japan Society for the Promotion of Science (JSPS)19H03171 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Short-lived intermediate in N 2 O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography.
Authors: Nomura, T. / Kimura, T. / Kanematsu, Y. / Yamada, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Murakami, H. / Hisano, T. / Yamagiwa, R. / Takeda, H. / Gopalasingam, C. / Kousaka, R. / ...Authors: Nomura, T. / Kimura, T. / Kanematsu, Y. / Yamada, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Murakami, H. / Hisano, T. / Yamagiwa, R. / Takeda, H. / Gopalasingam, C. / Kousaka, R. / Yanagisawa, S. / Shoji, O. / Kumasaka, T. / Yamamoto, M. / Takano, Y. / Sugimoto, H. / Tosha, T. / Kubo, M. / Shiro, Y.
History
DepositionJan 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP nitrous oxide-forming nitric oxide reductase
B: NADP nitrous oxide-forming nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,68712
Polymers88,8412
Non-polymers1,84610
Water10,665592
1
A: NADP nitrous oxide-forming nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3436
Polymers44,4211
Non-polymers9235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADP nitrous oxide-forming nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3436
Polymers44,4211
Non-polymers9235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.270, 101.610, 73.190
Angle α, β, γ (deg.)90.000, 92.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NADP nitrous oxide-forming nitric oxide reductase / NOR / CYPLVA1 / Cytochrome P450 55A1 / Cytochrome P450 DNIR / Cytochrome P450nor / Fungal nitric ...NOR / CYPLVA1 / Cytochrome P450 55A1 / Cytochrome P450 DNIR / Cytochrome P450nor / Fungal nitric oxide reductase


Mass: 44420.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: CYP55A1, CYP55 / Plasmid: pRSET-C / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P23295, nitric oxide reductase [NAD(P)+, nitrous oxide-forming]
#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-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
Details: 38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.23767 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 3, 2018
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23767 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 73309 / % possible obs: 100 % / Redundancy: 109.5 % / CC1/2: 0.987 / R split: 0.113 / Net I/σ(I): 6.76
Reflection shellResolution: 1.8→1.81 Å / Mean I/σ(I) obs: 1.88 / Num. unique obs: 1828 / CC1/2: 0.6 / R split: 0.622 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystFEL0.6.3data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
CrystFEL0.6.3data reduction
PHENIX1.18.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y5K

5y5k


Resolution: 1.8→19.78 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2191 3674 5.01 %
Rwork0.1727 69596 -
obs0.175 73270 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.53 Å2 / Biso mean: 27.3508 Å2 / Biso min: 11.84 Å2
Refinement stepCycle: final / Resolution: 1.8→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6198 0 136 592 6926
Biso mean--22.91 34.15 -
Num. residues----798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.820.30961480.268726542802
1.82-1.850.29691310.249626582789
1.85-1.880.24561550.241526872842
1.88-1.90.32311420.222526282770
1.9-1.930.28761190.207327112830
1.93-1.960.23971480.200726432791
1.96-20.24411410.19626892830
2-2.030.26691560.197526262782
2.03-2.070.2091470.18426692816
2.07-2.120.22761370.182526882825
2.12-2.160.24341290.181726832812
2.16-2.210.23971440.185826552799
2.21-2.270.23071420.184226782820
2.27-2.330.26811450.177126772822
2.33-2.40.21321570.171926412798
2.4-2.470.21871390.172226962835
2.47-2.560.23851370.178326732810
2.56-2.660.23071390.17526902829
2.66-2.790.22311390.168326492788
2.79-2.930.23071480.168526862834
2.93-3.120.22961370.166126762813
3.12-3.350.19941500.16126832833
3.35-3.690.19941380.154827022840
3.69-4.220.17611480.143426842832
4.22-5.30.16891230.150427242847
5.3-19.780.21551350.179727462881

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