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- PDB-4zfb: Cytochrome P450 pentamutant from BM3 bound to Palmitic Acid -

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Basic information

Entry
Database: PDB / ID: 4zfb
TitleCytochrome P450 pentamutant from BM3 bound to Palmitic Acid
ComponentsBifunctional P-450/NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Heme Oxidase Domain / Bacillus megaterium
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 / NICKEL (II) ION / PALMITIC ACID / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsRogers, W.E. / Othman, T. / Heidary, D.K. / Huxford, T.
CitationJournal: Biochemistry / Year: 2016
Title: Effect of Mutation and Substrate Binding on the Stability of Cytochrome P450BM3 Variants.
Authors: Geronimo, I. / Denning, C.A. / Rogers, W.E. / Othman, T. / Huxford, T. / Heidary, D.K. / Glazer, E.C. / Payne, C.M.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6718
Polymers53,5011
Non-polymers1,1707
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.679, 55.679, 707.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bifunctional P-450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3


Mass: 53500.973 Da / Num. of mol.: 1 / Fragment: UNP residues 1-461 / Mutation: R47L, F81I, F87V, L188Q, E267V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1, cyp102 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase

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Non-polymers , 5 types, 63 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 17.5mM NiCl2, 50mM PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.77→177.81 Å / Num. obs: 18183 / % possible obs: 97.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.4 / % possible all: 80.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHENIXphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NPL

3npl


Resolution: 2.84→117.929 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 845 5.06 %Random
Rwork0.2179 ---
obs0.2207 16706 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→117.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 69 56 3813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033843
X-RAY DIFFRACTIONf_angle_d0.7855204
X-RAY DIFFRACTIONf_dihedral_angle_d12.8661457
X-RAY DIFFRACTIONf_chiral_restr0.03557
X-RAY DIFFRACTIONf_plane_restr0.004675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8402-3.01820.37841300.30752322X-RAY DIFFRACTION91
3.0182-3.25130.31521580.26422527X-RAY DIFFRACTION98
3.2513-3.57850.29241310.2452614X-RAY DIFFRACTION100
3.5785-4.09630.29531280.21672673X-RAY DIFFRACTION100
4.0963-5.16090.25521380.19482722X-RAY DIFFRACTION100
5.1609-118.03120.22991600.19463003X-RAY DIFFRACTION100

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