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- PDB-1p0x: F393Y mutant heme domain of flavocytochrome P450 BM3 -

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Basic information

Entry
Database: PDB / ID: 1p0x
TitleF393Y mutant heme domain of flavocytochrome P450 BM3
ComponentsBifunctional P-450:NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / cytochrome P450 / fatty acid hydroxylase / monooxygenase
Function / homology
Function and homology information


aromatase activity / 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 / 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 / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Cytochrome p450 / Cytochrome P450 / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Cytochrome p450 / Cytochrome P450 / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / 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 / 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: 2 Å
AuthorsOst, T.W.B. / Clark, J. / Miles, C.S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. / Daff, S. / Mowat, C.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Oxygen Activation and Electron Transfer in Flavocytochrome P450 BM3
Authors: Ost, T.W.B. / Clark, J. / Mowat, C.G. / Miles, C.S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. / Daff, S.
History
DepositionApr 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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 1.4Aug 16, 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: Bifunctional P-450:NADPH-P450 reductase
B: Bifunctional P-450:NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6044
Polymers104,3712
Non-polymers1,2332
Water22,3031238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.608, 152.983, 61.774
Angle α, β, γ (deg.)90.00, 94.54, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein Bifunctional P-450:NADPH-P450 reductase / E.C.1.14.14.1 / heme domain of flavocytochrome P450 BM3 / Cytochrome P450(BM-3) / P450BM-3


Mass: 52185.461 Da / Num. of mol.: 2 / Fragment: Heme domain, residues 1-455 of SWS P14779 / Mutation: F393Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CYP102A21 / Plasmid: pCM126 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / 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.: 1238 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, PIPES, MAGNESIUM SULFATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMsodium PIPES1reservoirpH6.5-7.5
240 mM1reservoirMgSO4
318-21 %PEG80001reservoir
440 mg/mlprotein1drop
550 mMTris-HCl1drop
61 mMEDTA1droppH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.802 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 9, 2001
RadiationMonochromator: 0.8 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 2→17 Å / Num. all: 74261 / Num. obs: 67437 / % possible obs: 91 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.15 / Num. unique all: 6332 / % possible all: 85.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 17 Å / Num. measured all: 837703
Reflection shell
*PLUS
Highest resolution: 2 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2HPD

2hpd


Resolution: 2→17 Å / Cross valid method: thoughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3412 5.3 %random
Rwork0.1717 ---
all-67403 --
obs-63991 --
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7083 0 86 1238 8407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d2.6
X-RAY DIFFRACTIONp_angle_deg2.6
LS refinement shellResolution: 2→2.092 Å
RfactorNum. reflection
Rfree0.267 428
Rwork0.198 -
obs-7679
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 17 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d

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