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- PDB-1f25: CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ASN MUTANTS OF CYTOCHROM... -

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Basic information

Entry
Database: PDB / ID: 1f25
TitleCRYSTAL STRUCTURE OF NO COMPLEX OF THR243ASN MUTANTS OF CYTOCHROME P450NOR
ComponentsNITRIC OXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / nitric oxide reductase / Cytochrome P450nor
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 / Resolution: 1.4 Å
AuthorsShimizu, H. / Park, S.-Y.
Citation
Journal: J.Inorg.Biochem. / Year: 2000
Title: Mutation effects of a conserved threonine (Thr243) of cytochrome P450nor on its structure and function.
Authors: Obayashi, E. / Shimizu, H. / Park, S.Y. / Shoun, H. / Shiro, Y.
#1: 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.
#2: 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.
History
DepositionMay 23, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NITRIC OXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0414
Polymers44,3021
Non-polymers7393
Water10,395577
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.622, 81.933, 85.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NITRIC OXIDE REDUCTASE


Mass: 44302.496 Da / Num. of mol.: 1 / Mutation: T243N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Plasmid: PRSET-C / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P23295, nitric-oxide reductase
#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.: 577 / 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: 43.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG3350, MES, Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.2 / Details: Shimizu, H., (2000) J. Inorg. Biochem., 81, 191.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21 mMpotassium phosphate1drop
310 %(v/v)glycerol1drop
40.1 mMdithiothreitol1drop
50.1 mMEDTA1drop
636 %PEG40001reservoir
7100 mMMES1reservoir
810 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.6
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6 Å / Relative weight: 1
ReflectionResolution: 1.4→10 Å / Num. all: 685047 / Num. obs: 76306 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 9 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.129 / Num. unique all: 11024 / % possible all: 100
Reflection
*PLUS
Num. measured all: 685047
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 1.4→10 Å / σ(F): 0 / Stereochemistry target values: SHELX-97
RfactorNum. reflectionSelection details
Rfree0.204 3809 RANDOM
Rwork0.142 --
all-76046 -
obs-72237 -
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 51 577 3728
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.01
X-RAY DIFFRACTIONs_bond_d0.026
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.074

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