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- PDB-4due: cytochrome P450 BM3h-2G9C6 MRI sensor bound to serotonin -

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Basic information

Entry
Database: PDB / ID: 4due
Titlecytochrome P450 BM3h-2G9C6 MRI sensor bound to serotonin
Componentscytochrome P450 BM3 variant 2G9C6
KeywordsOXIDOREDUCTASE / cytochrome P450 / MRI contrast sensor / directed evolution
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 / SEROTONIN / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Sep 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_label_asym_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
A: cytochrome P450 BM3 variant 2G9C6
B: cytochrome P450 BM3 variant 2G9C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3106
Polymers107,7252
Non-polymers1,5854
Water14,952830
1
A: cytochrome P450 BM3 variant 2G9C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6553
Polymers53,8621
Non-polymers7932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cytochrome P450 BM3 variant 2G9C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6553
Polymers53,8621
Non-polymers7932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.609, 148.416, 64.029
Angle α, β, γ (deg.)90.00, 98.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein cytochrome P450 BM3 variant 2G9C6 / 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: 53862.285 Da / Num. of mol.: 2 / Fragment: heme domain, residues 1-465 / Mutation: R51C, F87L, T268A, L437Q, T438L
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / 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: 54.26 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium cacadylate, pH 5.5, 0.14 M Ca(Ac)2, 13 % PEG 8000, 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: May 18, 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: 1.7→38.41 Å / Num. all: 115043 / Num. obs: 115043 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.049 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.793.50.6511.258965169500.65198.3
1.79-1.93.40.411.853906159310.4197.5
1.9-2.033.20.2512.647586147650.25196.5
2.03-2.193.50.135.248444139780.1397.9
2.19-2.43.40.0848.243880128280.08497.7
2.4-2.693.30.05911.837713115550.05997
2.69-3.13.40.04117.435359102560.04197.8
3.1-3.83.20.0322.22653283820.0394.7
3.8-5.383.40.02227.72300967410.02297.9
5.38-38.413.30.0226.71222736570.0296.4

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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: 4DUD

4dud


Resolution: 1.7→38.41 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.711 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 5707 5 %RANDOM
Rwork0.1678 ---
all0.17 114028 --
obs0.17 114028 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.43 Å2 / Biso mean: 21.8807 Å2 / Biso min: 7.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20.36 Å2
2---0 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7232 0 112 830 8174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0227588
X-RAY DIFFRACTIONr_angle_refined_deg2.1592.00810295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395919
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50524.737361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.411151353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4111541
X-RAY DIFFRACTIONr_chiral_restr0.170.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215783
X-RAY DIFFRACTIONr_mcbond_it1.4191.54547
X-RAY DIFFRACTIONr_mcangle_it2.29827339
X-RAY DIFFRACTIONr_scbond_it3.64133041
X-RAY DIFFRACTIONr_scangle_it5.6084.52947
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 407 -
Rwork0.346 7995 -
all-8402 -
obs--96.69 %
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)
10.6432-0.14490.0660.42460.04990.27270.00190.04630.062-0.0163-0.0043-0.0046-0.01240.02160.00240.0066-0.0070.00180.0223-0.0060.0176-8.4665-0.602515.9211
20.8797-0.14050.0720.3326-0.16750.3079-0.00150.0885-0.01070.0233-0.0034-0.0025-0.0209-0.01350.00480.01750.0040.00810.0252-0.01360.018-20.78149.035917.714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 456
2X-RAY DIFFRACTION1A500 - 501
3X-RAY DIFFRACTION1A601 - 1031
4X-RAY DIFFRACTION2B2 - 456
5X-RAY DIFFRACTION2B500 - 501
6X-RAY DIFFRACTION2B601 - 999

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