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- PDB-2ij2: Atomic structure of the heme domain of flavocytochrome P450-BM3 -

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Basic information

Entry
Database: PDB / ID: 2ij2
TitleAtomic structure of the heme domain of flavocytochrome P450-BM3
ComponentsCytochrome P450 BM3
KeywordsOXIDOREDUCTASE / Cytochrome P450 / P450BM3 / monoxygenase / heme binding protein / atomic resolution
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Cytochrome p450 / Cytochrome P450 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHelen, H.S. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and spectroscopic characterization of P450 BM3 mutants with unprecedented P450 heme iron ligand sets. New heme ligation states influence conformational equilibria in P450 BM3.
Authors: Girvan, H.M. / Seward, H.E. / Toogood, H.S. / Cheesman, M.R. / Leys, D. / Munro, A.W.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_alt_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_alt_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.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: Cytochrome P450 BM3
B: Cytochrome P450 BM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5114
Polymers107,2782
Non-polymers1,2332
Water28,8961604
1
A: Cytochrome P450 BM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2562
Polymers53,6391
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 BM3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2562
Polymers53,6391
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.448, 153.426, 59.690
Angle α, β, γ (deg.)90.00, 94.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 BM3


Mass: 53639.098 Da / Num. of mol.: 2 / Fragment: Cytochrome P450 (Residues 1-470)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CYP102A1 / References: UniProt: P14779, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1604 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG and Magnesium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. all: 312598 / Num. obs: 312598 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BU7

1bu7


Resolution: 1.2→19.83 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.088 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.036 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16561 16593 5 %RANDOM
Rwork0.14779 ---
all0.1487 312598 --
obs0.1487 312598 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.713 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.04 Å2
2---0.14 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7337 0 86 1606 9029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227603
X-RAY DIFFRACTIONr_bond_other_d0.0010.026971
X-RAY DIFFRACTIONr_angle_refined_deg1.5172.00610313
X-RAY DIFFRACTIONr_angle_other_deg0.884316288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21724.708359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.254151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1551540
X-RAY DIFFRACTIONr_chiral_restr0.10.21133
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021448
X-RAY DIFFRACTIONr_nbd_refined0.230.21764
X-RAY DIFFRACTIONr_nbd_other0.1840.27138
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23700
X-RAY DIFFRACTIONr_nbtor_other0.0840.24102
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0940.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.279
X-RAY DIFFRACTIONr_mcbond_it1.6331.54874
X-RAY DIFFRACTIONr_mcbond_other0.7371.51796
X-RAY DIFFRACTIONr_mcangle_it2.05627364
X-RAY DIFFRACTIONr_scbond_it2.88733358
X-RAY DIFFRACTIONr_scangle_it3.7664.52945
X-RAY DIFFRACTIONr_rigid_bond_restr2.35316226
X-RAY DIFFRACTIONr_sphericity_free6.42231606
X-RAY DIFFRACTIONr_sphericity_bonded3.938314394
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 1206 -
Rwork0.29 23009 -
obs--100 %

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