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- PDB-5y5h: SF-ROX structure of cytochrome P450nor (NO-bound state) determine... -

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Basic information

Entry
Database: PDB / ID: 5y5h
TitleSF-ROX structure of cytochrome P450nor (NO-bound state) determined at SACLA
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
Model detailscytochrome P450nor in NO-bound state
AuthorsTosha, T. / Nomura, T. / Nishida, T. / Yamagiwa, R. / Yamashita, K. / Hirata, K. / Ueno, G. / Kimura, T. / Hisano, T. / Muramoto, K. ...Tosha, T. / Nomura, T. / Nishida, T. / Yamagiwa, R. / Yamashita, K. / Hirata, K. / Ueno, G. / Kimura, T. / Hisano, T. / Muramoto, K. / Sawai, H. / Takeda, H. / Yamashita, A. / Murakami, H. / Owada, S. / Tono, K. / Yabashi, M. / 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 2.1Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.classification
Revision 2.2Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
Water13,079726
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-28 kcal/mol
Surface area17580 Å2
Unit cell
Length a, b, c (Å)55.017, 75.570, 101.760
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.: 726 / 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: 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
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.2404 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jun 22, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2404 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 65042 / % possible obs: 94.7 % / Redundancy: 56.2 % / Biso Wilson estimate: 22.23 Å2 / CC1/2: 0.929 / Net I/σ(I): 47
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 8.6 / CC1/2: 0.602 / % possible all: 65.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
cctbx.xfeldata reduction
cctbx.primedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CL6

1cl6


Resolution: 1.5→24.452 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.46
RfactorNum. reflection% reflection
Rfree0.1956 3291 5.07 %
Rwork0.169 --
obs0.1703 64961 94.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.43 Å2 / Biso mean: 26.6776 Å2 / Biso min: 14.72 Å2
Refinement stepCycle: final / Resolution: 1.5→24.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 81 726 3910
Biso mean--23.99 36.98 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083326
X-RAY DIFFRACTIONf_angle_d0.9244550
X-RAY DIFFRACTIONf_chiral_restr0.056508
X-RAY DIFFRACTIONf_plane_restr0.007600
X-RAY DIFFRACTIONf_dihedral_angle_d13.9532061
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 (%)
1.5001-1.52150.3412910.31231742183365
1.5215-1.54420.3094940.29651957205172
1.5442-1.56830.36861050.28252070217577
1.5683-1.5940.26061120.26392188230082
1.594-1.62150.30111270.24832359248687
1.6215-1.6510.25151330.22122442257591
1.651-1.68270.24741440.22812569271396
1.6827-1.71710.25961470.20922668281599
1.7171-1.75440.21491380.188526942832100
1.7544-1.79520.24921540.180426692823100
1.7952-1.84010.20951380.175427232861100
1.8401-1.88980.19451340.165426882822100
1.8898-1.94540.21611450.171326892834100
1.9454-2.00820.18841580.170426702828100
2.0082-2.07990.19541470.16427112858100
2.0799-2.16310.19071480.161427182866100
2.1631-2.26150.18891420.154627112853100
2.2615-2.38060.17161430.160627252868100
2.3806-2.52960.17951500.163127152865100
2.5296-2.72470.20221450.16627272872100
2.7247-2.99850.20371430.16427512894100
2.9985-3.43140.15881580.159827682926100
3.4314-4.31930.17741460.150127922938100
4.3193-24.45510.19861490.168629243073100

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