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- PDB-4h24: Cytochrome P450BM3-CIS cyclopropanation catalyst -

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Basic information

Entry
Database: PDB / ID: 4h24
TitleCytochrome P450BM3-CIS cyclopropanation catalyst
ComponentsCytochrome P450-BM3 variant P450BM3-Cis
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Enzymatic Cyclopropanation / directed evolution / non-natural function
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 / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsCoelho, P.S. / Wang, Z.J. / Ener, M.E. / Baril, S.A. / Kannan, A. / Arnold, F.H. / Brustad, E.M.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: A serine-substituted P450 catalyzes highly efficient carbene transfer to olefins in vivo.
Authors: Coelho, P.S. / Wang, Z.J. / Ener, M.E. / Baril, S.A. / Kannan, A. / Arnold, F.H. / Brustad, E.M.
History
DepositionSep 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Dec 18, 2013Group: Structure summary
Revision 1.4Sep 20, 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.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 P450BM3-Cis
B: Cytochrome P450-BM3 variant P450BM3-Cis
C: Cytochrome P450-BM3 variant P450BM3-Cis
D: Cytochrome P450-BM3 variant P450BM3-Cis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,4198
Polymers214,9534
Non-polymers2,4664
Water3,549197
1
A: Cytochrome P450-BM3 variant P450BM3-Cis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3552
Polymers53,7381
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450-BM3 variant P450BM3-Cis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3552
Polymers53,7381
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450-BM3 variant P450BM3-Cis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3552
Polymers53,7381
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450-BM3 variant P450BM3-Cis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3552
Polymers53,7381
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.792, 62.745, 210.278
Angle α, β, γ (deg.)90.000, 115.750, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Cytochrome P450-BM3 variant P450BM3-Cis / Bifunctional P-450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Cytochrome P450 102


Mass: 53738.320 Da / Num. of mol.: 4 / Fragment: heme domain (UNP residues 1-464)
Mutation: V78A, F87V, P142S, T175I, A184V, S226R, H236Q, E252G, T268A, A290V, L353V, I366V, E442K
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1 M Bis-Tris, pH 5.2, 18% PEG3350, 0.2 M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→48.577 Å / Num. all: 75952 / Num. obs: 75952 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.053 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.642.60.395228434110810.39599.2
2.64-2.82.60.256326810104470.25699.2
2.8-2.992.60.1644.72537898840.16499.2
2.99-3.232.60.1017.52361191770.10199.2
3.23-3.542.60.06211.92171484410.06299
3.54-3.952.60.04216.81971176670.04298.7
3.95-4.562.60.03319.41720066980.03398.3
4.56-5.592.60.03120.31465557170.03198.5
5.59-7.912.60.0319.91135644430.0397.5
7.91-48.5772.50.02620.1605623970.02693.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JPZ CHAIN B

1jpz


Resolution: 2.5→48.577 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 22.351 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 3821 5 %RANDOM
Rwork0.1845 ---
all0.1877 75906 --
obs0.1877 75906 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.24 Å2 / Biso mean: 47.42 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å21.66 Å2
2--1.97 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14378 0 172 197 14747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02214921
X-RAY DIFFRACTIONr_angle_refined_deg1.72.00220267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87651819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43324.655696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.641152554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4511580
X-RAY DIFFRACTIONr_chiral_restr0.1090.22188
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111404
X-RAY DIFFRACTIONr_mcbond_it0.7471.59099
X-RAY DIFFRACTIONr_mcangle_it1.427214628
X-RAY DIFFRACTIONr_scbond_it2.29235822
X-RAY DIFFRACTIONr_scangle_it3.6544.55637
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 286 -
Rwork0.264 5279 -
all-5565 -
obs--99.14 %
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)
11.8299-0.5906-0.32421.10450.39780.5703-0.03970.0130.1049-0.040.0436-0.03060.01810.0463-0.00390.0947-0.02470.02210.07670.05050.0589-10.00730.012534.2754
22.4848-0.26740.01010.3816-0.01441.2695-0.03490.319-0.3234-0.03380.03810.0541-0.02840.0889-0.00320.0902-0.0530.03910.0846-0.03860.108825.9115-29.948612.4762
31.08770.2908-0.7480.6898-0.28411.619-0.06570.10240.0511-0.02570.12310.01950.0603-0.2353-0.05730.053-0.0479-0.0460.08280.06540.1181-53.9932-19.347960.472
40.63220.2284-0.25690.9351-0.67721.6088-0.10660.05460.0192-0.03890.0119-0.09960.0979-0.13420.09470.0335-0.02850.02580.11790.01510.0959-70.5003-40.2612103.8103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 457
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2B1 - 457
4X-RAY DIFFRACTION2B500
5X-RAY DIFFRACTION3C1 - 456
6X-RAY DIFFRACTION3C500
7X-RAY DIFFRACTION4D4 - 458
8X-RAY DIFFRACTION4D500

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