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- PDB-5y5g: Structure of cytochrome P450nor in NO-bound state: damaged by hig... -

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Basic information

Entry
Database: PDB / ID: 5y5g
TitleStructure of cytochrome P450nor in NO-bound state: damaged by high-dose (5.7 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: 1.36 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 1.1Jun 17, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 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

Downloads & links

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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
Water15,637868
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 area17660 Å2
Unit cell
Length a, b, c (Å)55.189, 75.477, 101.668
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
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.: 868 / 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: 48.39 %
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: May 18, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. obs: 87504 / % possible obs: 95.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 13.76 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.024 / Rrim(I) all: 0.066 / Χ2: 0.945 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.36-1.3870.6844840.840.2740.7340.88598.9
1.38-1.417.20.60545450.870.240.6520.87299.7
1.41-1.447.20.5645000.9090.2210.6030.90199.4
1.44-1.477.20.44245140.9260.1740.4750.92899.4
1.47-1.57.20.36645250.9560.1450.3940.93299.6
1.5-1.537.30.30145750.9680.1190.3230.93299.9
1.53-1.577.30.2645280.9730.1020.280.92699.8
1.57-1.617.30.22745620.9770.0890.2440.93299.8
1.61-1.667.30.18745010.9850.0730.2010.92999.9
1.66-1.717.30.15945940.9880.0630.1710.915100
1.71-1.777.40.13145530.9920.0520.1410.905100
1.77-1.857.40.10846050.9940.0420.1160.892100
1.85-1.936.30.09336620.9940.0380.11.03280.2
1.93-2.037.40.06846060.9980.0270.0740.866100
2.03-2.167.40.05545850.9980.0220.060.869100
2.16-2.336.20.06229170.9960.0260.0681.26663.3
2.33-2.567.40.05946270.9970.0230.0631.496100
2.56-2.937.40.04746790.9980.0180.0511.183100
2.93-3.697.10.03139520.9990.0120.0340.72484.1
3.69-506.80.02539900.9990.010.0270.54780.9

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Processing

Software
NameVersionClassification
SCALEPACK1.10.1_2155data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CL6

1cl6


Resolution: 1.36→26.972 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.63
RfactorNum. reflection% reflection
Rfree0.1662 4260 5 %
Rwork0.1333 --
obs0.1349 85186 92.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.46 Å2 / Biso mean: 20.0579 Å2 / Biso min: 8.19 Å2
Refinement stepCycle: final / Resolution: 1.36→26.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 81 868 4052
Biso mean--13.8 33.87 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083350
X-RAY DIFFRACTIONf_angle_d1.0284587
X-RAY DIFFRACTIONf_chiral_restr0.079513
X-RAY DIFFRACTIONf_plane_restr0.008603
X-RAY DIFFRACTIONf_dihedral_angle_d18.6161289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3597-1.37510.22351120.16122077218971
1.3751-1.39130.20671170.16432266238379
1.3913-1.40830.19981290.15792472260186
1.4083-1.42610.2171250.15462634275992
1.4261-1.44490.22121570.15012783294097
1.4449-1.46470.1881670.14282790295798
1.4647-1.48560.181480.13322891303999
1.4856-1.50780.16941330.12192842297599
1.5078-1.53130.19391470.119429103057100
1.5313-1.55640.17141630.119928302993100
1.5564-1.58330.151470.116228923039100
1.5833-1.6120.13621650.113128903055100
1.612-1.6430.15871490.10928763025100
1.643-1.67660.14411460.110628913037100
1.6766-1.7130.18181450.121728863031100
1.713-1.75290.1621450.118329033048100
1.7529-1.79670.14521730.118928643037100
1.7967-1.84530.16161450.122129203065100
1.8453-1.89950.181120.13822249236178
1.8995-1.96080.19391550.14252672282793
1.9608-2.03090.16881360.121229323068100
2.0309-2.11220.16851500.12129063056100
2.1122-2.20830.16761330.13282687282093
2.2083-2.32460.1655820.15141522160462
2.3246-2.47020.14711640.12629333097100
2.4702-2.66080.17921570.140929123069100
2.6608-2.92820.17981550.141129803135100
2.9282-3.35130.15411530.13629613114100
3.3513-4.21970.1481920.12551441153348
4.2197-26.97750.15971580.14853114327299

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