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- PDB-2uwh: Cytochrome P450 BM3 mutant in complex with palmitic acid -

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Basic information

Entry
Database: PDB / ID: 2uwh
TitleCytochrome P450 BM3 mutant in complex with palmitic acid
ComponentsBIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
KeywordsOXIDOREDUCTASE / FATTY-ACID BINDING / MULTIFUNCTIONAL ENZYME / METAL-BINDING / ELECTRON TRANSPORT / TRANSPORT / HYDROXYLASE / FLAVOPROTEIN / MONOOXYGENASE / FMN / FAD / NADP / IRON / HEME / REDOX / MEMBRANE / CYTOCHROME P450 BM3 MUTANT
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 / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm
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 / PALMITIC ACID / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBACILLUS MEGATERIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuang, W.-C. / Joyce, M.G. / Westlake, A.C.G. / Roberts, G.C.K. / Moody, P.C.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Filling a Hole in Cytochrome P450 Bm3 Improves Substrate Binding and Catalytic Efficiency.
Authors: Huang, W.-C. / Westlake, A.C.G. / Marechal, J.-D. / Joyce, M.G. / Moody, P.C.E. / Roberts, G.C.K.
History
DepositionMar 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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

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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
C: BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
D: BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
E: BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
F: BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,07418
Polymers314,8376
Non-polymers5,23712
Water9,350519
1
A: BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3463
Polymers52,4731
Non-polymers8732
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)53,3463
Polymers52,4731
Non-polymers8732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3463
Polymers52,4731
Non-polymers8732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3463
Polymers52,4731
Non-polymers8732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3463
Polymers52,4731
Non-polymers8732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3463
Polymers52,4731
Non-polymers8732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)116.827, 147.030, 183.402
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
BIFUNCTIONAL P-450\: NADPH-P450 REDUCTASE / CYTOCHROME P450BM3 / CYTOCHROME P450(BM-3) / P450BM-3


Mass: 52472.820 Da / Num. of mol.: 6 / Fragment: HEME DOMAIN, RESIDUES 1-458 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PALMITATE BOUND / Source: (gene. exp.) BACILLUS MEGATERIUM (bacteria) / Plasmid: PGLWBM3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P14779, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 82 TO PHE ENGINEERED RESIDUE IN CHAIN B, ALA 82 TO PHE ...ENGINEERED RESIDUE IN CHAIN A, ALA 82 TO PHE ENGINEERED RESIDUE IN CHAIN B, ALA 82 TO PHE ENGINEERED RESIDUE IN CHAIN C, ALA 82 TO PHE ENGINEERED RESIDUE IN CHAIN D, ALA 82 TO PHE ENGINEERED RESIDUE IN CHAIN E, ALA 82 TO PHE ENGINEERED RESIDUE IN CHAIN F, ALA 82 TO PHE

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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: 2.44 Å3/Da / Density % sol: 49.26 % / Description: NONE
Crystal growpH: 5
Details: 140 MM MGCL2, 25% POLYETHYLENE GLYCOL 2000MME AND 100 MM MESA, PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.8→73.5 Å / Num. obs: 76791 / % possible obs: 98 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.5 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JPZ

1jpz


Resolution: 2.8→114.71 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.84 / SU B: 18.329 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R: 1.527 / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 3858 5 %RANDOM
Rwork0.215 ---
obs0.219 72833 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.52 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.8→114.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22140 0 366 519 23025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02223058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.98731218
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98352742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83224.8391116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.581154086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.01915120
X-RAY DIFFRACTIONr_chiral_restr0.0840.23306
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217592
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.211921
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.215692
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2956
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.2144
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.409 303
Rwork0.273 4997

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