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- PDB-5y5f: Structure of cytochrome P450nor in NO-bound state: damaged by low... -

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Basic information

Entry
Database: PDB / ID: 5y5f
TitleStructure of cytochrome P450nor in NO-bound state: damaged by low-dose (0.72 MGy) X-ray
ComponentsNADP nitrous oxide-forming nitric oxide reductase
KeywordsOXIDOREDUCTASE / metal-binding
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 / 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 / NITRIC OXIDE / NADP nitrous oxide-forming nitric oxide reductase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
Model detailscytochrome P450nor low dose data
AuthorsTosha, T. / Nomura, T. / Nishida, T. / Ueno, G. / Murakami, H. / Yamashita, K. / Hirata, K. / Yamamoto, M. / Ago, H. / Sugimoto, H. ...Tosha, T. / Nomura, T. / Nishida, T. / Ueno, G. / Murakami, H. / Yamashita, K. / Hirata, K. / Yamamoto, M. / Ago, H. / Sugimoto, H. / Shiro, Y. / Kubo, M.
CitationJournal: Nat Commun / Year: 2017
Title: Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Authors: Tosha, T. / Nomura, T. / Nishida, T. / Saeki, N. / Okubayashi, K. / Yamagiwa, R. / Sugahara, M. / Nakane, T. / Yamashita, K. / Hirata, K. / Ueno, G. / Kimura, T. / Hisano, T. / Muramoto, K. ...Authors: Tosha, T. / Nomura, T. / Nishida, T. / Saeki, N. / Okubayashi, K. / Yamagiwa, R. / Sugahara, M. / Nakane, T. / Yamashita, K. / Hirata, K. / Ueno, G. / Kimura, T. / Hisano, T. / Muramoto, K. / Sawai, H. / Takeda, H. / Mizohata, E. / Yamashita, A. / Kanematsu, Y. / Takano, Y. / Nango, E. / Tanaka, R. / Nureki, O. / Shoji, O. / Ikemoto, Y. / Murakami, H. / Owada, S. / Tono, K. / Yabashi, M. / Yamamoto, M. / Ago, H. / Iwata, S. / Sugimoto, H. / Shiro, Y. / Kubo, M.
History
DepositionAug 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,1594
Polymers44,4211
Non-polymers7393
Water13,385743
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-27 kcal/mol
Surface area17590 Å2
Unit cell
Length a, b, c (Å)54.916, 75.667, 101.811
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 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.: 1 / Fragment: nitric-oxide reductase cytochrome P450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: CYP55A1, CYP55 / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 17% PEG 10000, 0.1 M BIS-TRIS 0.1 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 6, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 67790 / % possible obs: 99.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 13.38 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Χ2: 0.878 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.535.20.51733130.8630.2370.5710.73698
1.53-1.555.30.46632750.8720.2120.5140.76198.8
1.55-1.585.30.433440.90.1810.4410.76998.2
1.58-1.625.30.35432970.9050.1610.3910.78298.7
1.62-1.655.30.30333210.9240.1370.3340.79898.9
1.65-1.695.40.26833350.9330.1210.2950.77999
1.69-1.735.40.23133610.9410.1040.2540.78399.4
1.73-1.785.40.19933760.9570.0890.2190.79899.6
1.78-1.835.50.16833670.9680.0760.1850.79799.5
1.83-1.895.50.14733850.9720.0660.1620.85599.9
1.89-1.965.60.1333590.9730.0580.1420.88699.9
1.96-2.045.60.1133960.980.0490.1210.928100
2.04-2.135.70.133950.9810.0440.110.975100
2.13-2.245.70.09133810.9850.040.0991.009100
2.24-2.385.70.08434430.9850.0370.0921.042100
2.38-2.565.80.0834000.9880.0350.0881.089100
2.56-2.825.80.0734640.990.0310.0771.019100
2.82-3.235.90.06334500.9920.0270.0691.003100
3.23-4.0760.05934950.9940.0240.0641.015100
4.07-305.70.04436330.9960.0190.0490.6399

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CL6

1cl6


Resolution: 1.5→26.973 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3
RfactorNum. reflection% reflection
Rfree0.1856 3424 5.09 %
Rwork0.1605 --
obs0.1618 67309 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.94 Å2 / Biso mean: 17.9416 Å2 / Biso min: 6.57 Å2
Refinement stepCycle: final / Resolution: 1.5→26.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 81 743 3927
Biso mean--13.67 31.06 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013340
X-RAY DIFFRACTIONf_angle_d1.0494572
X-RAY DIFFRACTIONf_chiral_restr0.062511
X-RAY DIFFRACTIONf_plane_restr0.008602
X-RAY DIFFRACTIONf_dihedral_angle_d13.3252083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5004-1.52180.2411080.20652023213175
1.5218-1.54450.22041310.19582527265895
1.5445-1.56870.20371400.18852597273797
1.5687-1.59440.23371410.18172590273198
1.5944-1.62190.20821380.18462653279198
1.6219-1.65140.22361430.18262634277798
1.6514-1.68310.21421380.17922650278899
1.6831-1.71750.22611500.18032674282499
1.7175-1.75480.22811390.185526702809100
1.7548-1.79560.20581510.179226622813100
1.7956-1.84050.18061390.174926942833100
1.8405-1.89030.18581350.167927022837100
1.8903-1.94590.19751440.167126792823100
1.9459-2.00870.17591580.169326652823100
2.0087-2.08040.21011480.164627052853100
2.0804-2.16370.17981470.159627162863100
2.1637-2.26210.17371410.152827122853100
2.2621-2.38130.17111430.157727242867100
2.3813-2.53040.1571510.157226992850100
2.5304-2.72560.20411430.164227382881100
2.7256-2.99960.20281450.156127372882100
2.9996-3.43290.15731580.152327642922100
3.4329-4.32220.17031450.135127812926100
4.3222-26.97710.1741480.15122889303799

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