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- PDB-4dtw: cytochrome P450 BM3h-8C8 MRI sensor bound to serotonin -

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Basic information

Entry
Database: PDB / ID: 4dtw
Titlecytochrome P450 BM3h-8C8 MRI sensor bound to serotonin
ComponentsCytochrome P450 BM3 variant 8C8
KeywordsOXIDOREDUCTASE / cytochrome P450 / MRI contrast sensor / directed evolution
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 / SEROTONIN / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBrustad, E.M. / Lelyveld, V.S. / Snow, C.D. / Crook, N. / Martinez, F.M. / Scholl, T.J. / Jasanoff, A. / Arnold, F.H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structure-guided directed evolution of highly selective p450-based magnetic resonance imaging sensors for dopamine and serotonin.
Authors: Brustad, E.M. / Lelyveld, V.S. / Snow, C.D. / Crook, N. / Jung, S.T. / Martinez, F.M. / Scholl, T.J. / Jasanoff, A. / Arnold, F.H.
History
DepositionFeb 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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_ref_seq_dif / 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_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.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.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.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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
B: Cytochrome P450 BM3 variant 8C8
A: Cytochrome P450 BM3 variant 8C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9427
Polymers107,3322
Non-polymers1,6105
Water19,0241056
1
B: Cytochrome P450 BM3 variant 8C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4834
Polymers53,6661
Non-polymers8173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Cytochrome P450 BM3 variant 8C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4593
Polymers53,6661
Non-polymers7932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.606, 146.249, 64.064
Angle α, β, γ (deg.)90.000, 97.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 BM3 variant 8C8 / Bifunctional P-450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Cytochrome ...Bifunctional P-450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Cytochrome P450 102 / NADPH-cytochrome P450 reductase


Mass: 53665.984 Da / Num. of mol.: 2 / Fragment: heme domain, residues 1-465 / Mutation: L75P, Q189R, I263A, T268A, V286E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CYP102A1, cyp102 / Production host: Escherichia coli (E. coli) / 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-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O / Comment: neurotransmitter*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1056 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.2 M MgCl2, 22 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2011
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→38.874 Å / Num. all: 91179 / Num. obs: 91179 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.078 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.92.40.581.132300136560.5895
1.9-2.012.30.4620.929904127510.46293.8
2.01-2.152.30.2582.726587116800.25891.6
2.15-2.322.40.1594.627326113110.15994.9
2.32-2.552.40.116.624926103410.1194.2
2.55-2.852.30.0789.22098789330.07890.2
2.85-3.292.40.05212.81990081420.05292.8
3.29-4.022.40.0415.61520264530.0487
4.02-5.692.50.03516.31269051310.03589.6
5.69-38.8742.40.03314.8674227810.03387.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XSCALEdata scaling
MOLREP(ccp4 6.1)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DTZ

4dtz


Resolution: 1.8→38.87 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.138 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4678 5.1 %RANDOM
Rwork0.1917 86403 --
obs0.1949 91081 92.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.66 Å2 / Biso mean: 22.834 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20.21 Å2
2---0.74 Å2-0 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7298 0 113 1056 8467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0227610
X-RAY DIFFRACTIONr_angle_refined_deg1.9712.00710320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7595908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.924.785372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.747151344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8671542
X-RAY DIFFRACTIONr_chiral_restr0.140.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215838
X-RAY DIFFRACTIONr_mcbond_it1.1991.54544
X-RAY DIFFRACTIONr_mcangle_it1.87227336
X-RAY DIFFRACTIONr_scbond_it3.14333066
X-RAY DIFFRACTIONr_scangle_it4.674.52982
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 340 -
Rwork0.366 6559 -
all-6899 -
obs--95.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.00020.1098-0.04350.26420.07310.1660.0041-0.0519-0.06760.00530.0068-0.0393-0.0098-0.0014-0.0110.020.0013-0.00090.01720.0040.00916.5683-0.102314.1682
20.78960.09240.01770.4316-0.18380.2091-0.0009-0.06450.04990.01690.00880.00390.0052-0.0158-0.00790.0253-0.0041-0.00340.0247-0.00510.00444.505-49.314815.6444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 455
2X-RAY DIFFRACTION1B501 - 503
3X-RAY DIFFRACTION1B601 - 1133
4X-RAY DIFFRACTION2A3 - 455
5X-RAY DIFFRACTION2A500 - 501
6X-RAY DIFFRACTION2A601 - 1123

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