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- PDB-4duc: cytochrome P450 BM3h-2G9 MRI sensor, no ligand -

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Basic information

Entry
Database: PDB / ID: 4duc
Titlecytochrome P450 BM3h-2G9 MRI sensor, no ligand
Componentscytochrome P450 BM3 variant 2G9
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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 2G9
B: cytochrome P450 BM3 variant 2G9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1904
Polymers107,9572
Non-polymers1,2332
Water10,233568
1
A: cytochrome P450 BM3 variant 2G9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5952
Polymers53,9791
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cytochrome P450 BM3 variant 2G9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5952
Polymers53,9791
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.655, 153.748, 60.978
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein cytochrome P450 BM3 variant 2G9 / 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: 53978.504 Da / Num. of mol.: 2 / Fragment: heme domain, residues 1-465 / Mutation: R51C, F87L, T268A, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
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, 14 % 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 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2010
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→29.224 Å / Num. all: 78209 / Num. obs: 78209 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.089 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.92-2.0230.4251.12812994290.42578.9
2.02-2.153.40.4380.938084110940.43898.3
2.15-2.293.30.3430.934812103980.34398.1
2.29-2.483.50.1354.93411397420.13598.5
2.48-2.713.50.1353.23115089700.13598.6
2.71-3.033.50.08172793080610.08197.7
3.03-3.53.50.0723.82520272220.07299.3
3.5-4.293.50.0576.72112660370.05798.3
4.29-6.073.50.0316.11627546640.0397.5
6.07-29.2243.50.02120.1915025920.02197.7

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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: 2IJ2

2ij2


Resolution: 1.92→29.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.935 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 3864 5 %RANDOM
Rwork0.1849 ---
all0.187 77407 --
obs0.187 77407 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.48 Å2 / Biso mean: 20.0628 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å21.36 Å2
2---1 Å20 Å2
3---2.68 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7242 0 86 568 7896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227542
X-RAY DIFFRACTIONr_angle_refined_deg1.912.00410246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72824.749358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.977151306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5311540
X-RAY DIFFRACTIONr_chiral_restr0.130.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215776
X-RAY DIFFRACTIONr_mcbond_it1.0581.54572
X-RAY DIFFRACTIONr_mcangle_it1.81427369
X-RAY DIFFRACTIONr_scbond_it3.14532970
X-RAY DIFFRACTIONr_scangle_it4.7414.52873
LS refinement shellResolution: 1.924→1.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 180 -
Rwork0.303 3984 -
all-4164 -
obs--69.77 %
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)
10.7337-0.3168-0.14281.128-0.10480.3230.0507-0.0018-0.0647-0.047-0.02850.0951-0.02460.0399-0.02220.0177-0.0022-0.00190.0197-0.01630.02199.63380.063720.9279
21.1541-0.2637-0.25010.69410.21950.43070.00690.13790.0524-0.0508-0.01550.0194-0.0058-0.02970.00860.01410.00140.00310.03960.02880.026421.3914-49.513412.6107
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 457
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A601 - 884
4X-RAY DIFFRACTION2B2 - 457
5X-RAY DIFFRACTION2B500
6X-RAY DIFFRACTION2B601 - 884

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