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- PDB-1jfb: X-ray structure of nitric oxide reductase (cytochrome P450nor) in... -

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Basic information

Entry
Database: PDB / ID: 1jfb
TitleX-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferric resting state at atomic resolution
Componentsnitric-oxide reductase cytochrome P450 55A1
KeywordsOXIDOREDUCTASE / nitric oxide reductase / Cytochrome P450nor / atomic resolution / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsShimizu, H. / Adachi, S. / Park, S.Y. / Shiro, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution.
Authors: Shimizu, H. / Park, S.Y. / Shiro, Y. / Adachi, S.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum
Authors: Park, S.Y. / Shimizu, H. / Adachi, S. / Nakagawa, A. / Tanaka, I. / Nakahara, K. / Shoun, H. / Obayashi, E. / Nakamura, H. / Iizuka, T. / Shiro, Y.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: Proton Delivery in No Reduction by Fungal Nitric-Oxide Reductase. Cryogenic Crystallography, Spectroscopy, and Kinetics of Ferric-No Complexes of Wild- Type and Mutant Enzymes
Authors: Shimizu, H. / Obayashi, E. / Gomi, Y. / Arakawa, H. / Park, S.Y. / Nakamura, H. / Adachi, S. / Shoun, H. / Shiro, Y.
History
DepositionJun 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nitric-oxide reductase cytochrome P450 55A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2303
Polymers44,5221
Non-polymers7092
Water18,8081044
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.661, 82.132, 85.843
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein nitric-oxide reductase cytochrome P450 55A1


Mass: 44521.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / References: UniProt: P23295, nitric-oxide reductase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 1044 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG3350, MES, Glycerol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Details: used microseeding / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
136 %PEG40001reservoir
20.1 MMES1reservoir
310 %glycerol1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 1999
RadiationMonochromator: Si(111) flat / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1→100 Å / Num. all: 1745175 / Num. obs: 204021 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 7.1
Reflection shellResolution: 1→1.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 3.5 / Num. unique all: 29073 / % possible all: 96.6
Reflection
*PLUS
Highest resolution: 1 Å / Lowest resolution: 100 Å / Num. measured all: 1745175
Reflection shell
*PLUS
% possible obs: 96.6 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→10 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.139 10117 -RANDOM
Rwork0.102 ---
all-203704 --
obs-203704 98 %-
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 49 1044 4192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1 Å / Lowest resolution: 10 Å / Num. reflection obs: 38979 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.102
Solvent computation
*PLUS
Displacement parameters
*PLUS

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