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- PDB-2j4s: P450 BM3 heme domain in complex with DMSO -

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Basic information

Entry
Database: PDB / ID: 2j4s
TitleP450 BM3 heme domain in complex with DMSO
ComponentsBIFUNCTIONAL P-450\:NADPH-P450 REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / MONOOXYGENASE / METAL-BINDING / P450 / IRON / HEME / DMSO-INHIBITION / ORGANIC SOLVENT
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 / DI(HYDROXYETHYL)ETHER / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBACILLUS MEGATERIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKuper, J. / Tuck-Seng, W. / Roccatano, D. / Wilmanns, M. / Schwaneberg, U.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Understanding a Mechanism of Organic Cosolvent Inactivation in Heme Monooxygenase P450 Bm-3.
Authors: Kuper, J. / Wong, T.S. / Roccatano, D. / Wilmanns, M. / Schwaneberg, U.
History
DepositionSep 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)106,16810
Polymers104,3392
Non-polymers1,8298
Water8,197455
1
A: BIFUNCTIONAL P-450\:NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9984
Polymers52,1691
Non-polymers8293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BIFUNCTIONAL P-450\:NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1706
Polymers52,1691
Non-polymers1,0005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.598, 88.297, 151.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2263, 0.9409, 0.2521), (-0.9349, 0.1372, 0.3272), (0.2733, -0.3097, 0.9107)
Vector: 13.22, -29.6, 15.72)

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Components

#1: Protein BIFUNCTIONAL P-450\:NADPH-P450 REDUCTASE / BM3 P450 / CYTOCHROME P450 / BM-3 / P450BM-3


Mass: 52169.461 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, RESIDUES 1-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS MEGATERIUM (bacteria) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.6 Å3/Da / Density % sol: 52.64 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 2.09→23.48 Å / Num. obs: 62273 / % possible obs: 97.4 % / Redundancy: 3.53 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.34
Reflection shellResolution: 2.09→2.11 Å / Redundancy: 3.21 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.04 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→21.78 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.842 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3151 5.15 %RANDOM
Rwork0.19 ---
obs0.193 62217 99 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 27.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.075 Å20 Å20 Å2
2---0.127 Å20 Å2
3---0.052 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7283 0 122 455 7860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227589
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5552.00510266
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20624.837368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.512151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8321540
X-RAY DIFFRACTIONr_chiral_restr0.1040.21092
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025758
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.24239
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25252
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2679
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.841.54610
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41227296
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.36433310
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5954.52965
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 8.66→21.78 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 38
Rwork0.198 876

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