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- PDB-1gei: STRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CY... -

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Basic information

Entry
Database: PDB / ID: 1gei
TitleSTRUCTURAL CHARACTERIZATION OF N-BUTYL-ISOCYANIDE COMPLEXES OF CYTOCHROMES P450NOR AND P450CAM
ComponentsCYTOCHROME P450 55A1
KeywordsOXIDOREDUCTASE / Cytocrome P450nor (Fe-II) / Isocyanide Complexe form
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 / N-BUTYL ISOCYANIDE / NADP nitrous oxide-forming nitric oxide reductase
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLee, D.-S. / Park, S.-Y. / Yamane, K. / Shiro, Y.
Citation
Journal: Biochemistry / Year: 2001
Title: Structural characterization of n-butyl-isocyanide complexes of cytochromes P450nor and P450cam.
Authors: Lee, D.S. / Park, S.Y. / Yamane, K. / Obayashi, E. / Hori, H. / Shiro, Y.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of nitric oxide reductase from denitrifing 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
DepositionNov 13, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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 55A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1203
Polymers44,4211
Non-polymers7002
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.750, 81.640, 86.230
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


Mass: 44420.691 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) / Strain (production host): JM109
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: Chemical ChemComp-NBN / N-BUTYL ISOCYANIDE


Mass: 83.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Details: Park, S-Y., (1997) FEBS. Lett., 412, 346.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
220 mMpotassium phosphate1drop
310 %(v/v)glycerol1drop
40.1 mMdithiothreitol1drop
50.1 mMEDTA1drop
6100 mMMES1reservoir
7PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2000 / Details: mirrors
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 289017 / Num. obs: 47202 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5926 / % possible all: 81
Reflection shell
*PLUS
% possible obs: 81 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ROM

1rom


Resolution: 1.6→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2372 -RANDOM
Rwork0.207 ---
all-47158 --
obs--91.2 %-
Displacement parametersBiso mean: 18.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 49 285 3433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_improper_angle_d0.77
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.306 324 -
Rwork0.302 --
obs-6824 80.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.77

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