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- PDB-1xqd: Crystal structure of P450NOR complexed with 3-pyridinealdehyde ad... -

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Basic information

Entry
Database: PDB / ID: 1xqd
TitleCrystal structure of P450NOR complexed with 3-pyridinealdehyde adenine dinucleotide
ComponentsCYTOCHROME P450 55A1
KeywordsOXIDOREDUCTASE / NITRIC OXIDE REDUCTASE / CYTOCHROME P450NOR / NADH COMPLEX
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
NICOTINIC ACID ADENINE DINUCLEOTIDE / 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: 1.8 Å
AuthorsOshima, R. / Fushinobu, S. / Takaya, N. / Su, F. / Wakagi, T. / Shoun, H.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural evidence for direct hydride transfer from NADH to cytochrome P450nor
Authors: Oshima, R. / Fushinobu, S. / Su, F. / Zhang, L. / Takaya, N. / Shoun, H.
History
DepositionOct 12, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME P450 55A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6423
Polymers44,3601
Non-polymers1,2822
Water8,881493
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.296, 56.121, 163.262
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 55A1 / P450nor


Mass: 44359.660 Da / Num. of mol.: 1 / Mutation: S73G/S75G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Plasmid: PRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / 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-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 1.93 Å3/Da / Density % sol: 35.7 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 8000, sodium acetate, sodium cacodylate, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9712
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2003
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9712 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 36884 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 31
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 18.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EHE

1ehe


Resolution: 1.8→19.54 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1828 5 %RANDOM
Rwork0.206 ---
all0.208 37717 --
obs0.206 36850 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4906 Å2 / ksol: 0.37388 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.43 Å20 Å20 Å2
2---1.41 Å20 Å2
3----6.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 87 493 3675
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d1.33
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.42
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.552.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 304 5 %
Rwork0.222 5781 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEMPAD.PARAMHEMPAD2.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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