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- PDB-5y5l: Time-resolved SFX structure of cytochrome P450nor: dark-2 data in... -

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Basic information

Entry
Database: PDB / ID: 5y5l
TitleTime-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state)
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 / NADP nitrous oxide-forming nitric oxide reductase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Model detailscytochrome P450nor
AuthorsTosha, T. / Nomura, T. / Nishida, T. / Saeki, N. / Okubayashi, K. / Yamagiwa, R. / Sugahara, M. / Nakane, T. / Yamashita, K. / Hirata, K. ...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. / Ikemoto, Y. / Murakami, H. / Owada, S. / Tono, K. / Yabashi, M. / Yamamoto, M. / Ago, H. / Iwata, S. / 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 1.1Sep 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Nov 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
B: NADP nitrous oxide-forming nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0744
Polymers88,8412
Non-polymers1,2332
Water7,278404
1
A: NADP nitrous oxide-forming nitric oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0372
Polymers44,4211
Non-polymers6161
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)45,0372
Polymers44,4211
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.600, 102.300, 73.700
Angle α, β, γ (deg.)90.000, 92.600, 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 (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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5
Details: 34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Dec 6, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 47209 / % possible obs: 100 % / Redundancy: 923.9 % / Biso Wilson estimate: 43.53 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.12 Å / Redundancy: 639.2 % / Mean I/σ(I) obs: 1.4 / CC1/2: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CL6

1cl6


Resolution: 2.1→19.919 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.04
RfactorNum. reflection% reflection
Rfree0.1926 2345 4.98 %
Rwork0.1459 --
obs0.1481 47126 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.53 Å2 / Biso mean: 45.6197 Å2 / Biso min: 26.86 Å2
Refinement stepCycle: final / Resolution: 2.1→19.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6198 0 86 404 6688
Biso mean--36.45 50.94 -
Num. residues----798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086470
X-RAY DIFFRACTIONf_angle_d0.9648831
X-RAY DIFFRACTIONf_chiral_restr0.054991
X-RAY DIFFRACTIONf_plane_restr0.0061159
X-RAY DIFFRACTIONf_dihedral_angle_d11.5353989
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.14280.34411340.320425902724
2.1428-2.18940.2871340.25826552789
2.1894-2.24020.27881300.218126062736
2.2402-2.29620.24271440.195126342778
2.2962-2.35820.23531490.178826072756
2.3582-2.42740.22231480.179726192767
2.4274-2.50560.23711390.170126032742
2.5056-2.5950.21741370.167426392776
2.595-2.69870.23921370.163726232760
2.6987-2.82120.22721260.166726542780
2.8212-2.96940.23991490.158726122761
2.9694-3.15480.23631420.153426422784
3.1548-3.39730.20421420.146826472789
3.3973-3.73710.17891330.1326462779
3.7371-4.27330.14821470.113326362783
4.2733-5.36640.13611200.115826722792
5.3664-19.920.15121340.133426962830

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