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- PDB-1rom: CRYSTAL STRUCTURE OF NITRIC REDUCTASE FROM DENITRIFYING FUNGUS FU... -

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Basic information

Entry
Database: PDB / ID: 1rom
TitleCRYSTAL STRUCTURE OF NITRIC REDUCTASE FROM DENITRIFYING FUNGUS FUSARIUM OXYSPORUM
ComponentsCYTOCHROME P450
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 / NADP nitrous oxide-forming nitric oxide reductase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsPark, S.-Y. / Nakagawa, A.
CitationJournal: 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
DepositionMar 24, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _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: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0372
Polymers44,4211
Non-polymers6161
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.990, 82.660, 87.210
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 CYTOCHROME P450 / / CYTOCHROME P450NOR / NITRIC OXIDE REDUCTASE


Mass: 44420.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus)
References: UniProt: P23295, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.2 Å3/Da / Density % sol: 41 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD, ANOMALOUS DISPERSION EFFECT OF HEME IRON WAS INCLUDED FOR PHASE CALCULATION.
Crystal growpH: 5.5
Details: PROTEIN WAS CRYSTALLIZED FROM 100MM-MES BUFFER AT PH5.5 USING PEG4000 AS PRECIPITANT
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Park, S.Y., (1997) FEBS Lett. 412, 346.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMMES1reservoir
225 mg/mlprotein1drop
350 mMMES1drop
4PEG40001reservoir
5PEG40001drop

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 10, 1995 / Details: MIRROR/MONOCHROMATOR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 24733 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 7 / % possible all: 79.5
Reflection
*PLUS
Num. measured all: 84152
Reflection shell
*PLUS
% possible obs: 79.5 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALAdata scaling
Agrovatadata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1252 5.1 %RANDOM
Rwork0.197 ---
obs0.197 24490 89.8 %-
Displacement parametersBiso mean: 18.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 43 159 3301
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.051.5
X-RAY DIFFRACTIONx_mcangle_it3.072
X-RAY DIFFRACTIONx_scbond_it42
X-RAY DIFFRACTIONx_scangle_it5.972.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.316 133 5.3 %
Rwork0.253 2367 -
obs--74.6 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32

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