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- PDB-3qi8: Evolved variant of cytochrome P450 (BM3, CYP102A1) -

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Basic information

Entry
Database: PDB / ID: 3qi8
TitleEvolved variant of cytochrome P450 (BM3, CYP102A1)
ComponentsEvolved Cytochrome P450 variant (22A3)
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Oxidation (Naproxen / Ibuprofen)
Function / homologyCytochrome p450 / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRentmeister, A. / Brown, T.R. / Snow, C.D. / Carbone, M.N. / Arnold, F.H.
CitationJournal: Chemcatchem / Year: 2011
Title: Engineered Bacterial Mimics of Human Drug Metabolizing Enzyme CYP2C9
Authors: Rentmeister, A. / Brown, T.R. / Snow, C.D. / Carbone, M.N. / Arnold, F.H.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Evolved Cytochrome P450 variant (22A3)
A: Evolved Cytochrome P450 variant (22A3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5494
Polymers108,3162
Non-polymers1,2332
Water0
1
B: Evolved Cytochrome P450 variant (22A3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7742
Polymers54,1581
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Evolved Cytochrome P450 variant (22A3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7742
Polymers54,1581
Non-polymers6161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.350, 83.770, 143.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B and (resseq 2:9 or resseq 14:71 or resseq...
211chain A and (resseq 2:9 or resseq 14:71 or resseq...

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Components

#1: Protein Evolved Cytochrome P450 variant (22A3)


Mass: 54157.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (gene. exp.) Bacillus megaterium (bacteria) / Production host: Escherichia coli (E. coli) / References: unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Sequence detailsTHIS SEQUENCE EVOLVED FROM CYP102A1(UNP P14779) VIA VARIANTS 5H6 AND 13C9

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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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate, PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 5, 2009 / Details: double mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→45.4 Å / Num. all: 18561 / Num. obs: 17710 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)% possible all
3.1-3.2794
3.27-3.4795.7
3.47-3.7196.3
3.71-496.8
4-4.3896.6
4.38-4.996.5
4.9-5.6696.8
5.66-6.9396.9
6.93-9.897
9.8-45.495.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JPZ

1jpz


Resolution: 3.2→45.384 Å / SU ML: 0.43 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 840 5.2 %random
Rwork0.2082 ---
obs0.2115 16147 95.54 %-
all-18561 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.44 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1537 Å20 Å20 Å2
2---2.3667 Å20 Å2
3---2.213 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6994 0 86 0 7080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017246
X-RAY DIFFRACTIONf_angle_d1.4099821
X-RAY DIFFRACTIONf_dihedral_angle_d20.942706
X-RAY DIFFRACTIONf_chiral_restr0.0821059
X-RAY DIFFRACTIONf_plane_restr0.0071271
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3203X-RAY DIFFRACTIONPOSITIONAL
12A3203X-RAY DIFFRACTIONPOSITIONAL0.065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.40060.30521530.26532427X-RAY DIFFRACTION94
3.4006-3.6630.29631310.22832512X-RAY DIFFRACTION95
3.663-4.03140.28151470.20312538X-RAY DIFFRACTION96
4.0314-4.61430.26651370.18072546X-RAY DIFFRACTION96
4.6143-5.81160.27221390.1932564X-RAY DIFFRACTION96
5.8116-45.38810.24721330.19572720X-RAY DIFFRACTION96
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)
12.21611.0383-0.3021-0.6567-1.0153.3532-0.9381.18751.2473-1.28050.51690.524-0.1156-0.43610.00111.1454-0.4832-0.50661.10110.4181.1895-32.5871-15.951-44.1056
26.30890.5583-0.06271.00471.7024.4402-0.63290.4480.3288-0.05550.87540.5266-0.21450.4182-0.00280.2091-0.04780.09320.49340.14480.0871-26.9872-23.2368-9.9864
30.974-1.4092-0.09821.26010.01271.00840.3995-0.3704-0.6934-1.57760.35451.87411.5147-2.54450.05890.6622-0.2329-0.08261.17890.27941.1551-45.3513-22.8504-17.7269
4-0.0692-0.4611-2.07360.95660.9720.32431.3498-0.25781.1590.93180.06720.1768-1.42150.00960.00011.2566-0.2630.33460.99160.10541.1122-34.9566-6.5771-7.7734
51.89961.70810.41621.69141.20332.993-0.20050.55850.5854-0.9401-0.00930.03320.0824-0.05370.01250.4573-0.0930.02540.46650.16480.4652-20.0858-21.7629-27.8296
64.2249-0.64042.39533.3185-1.2686.0233-0.11770.1537-0.017-0.41630.00010.16020.15410.3298-0.00020.31150.03240.11430.545-0.00580.2495-21.138-28.0609-21.1396
71.7873-0.83362.69332.1868-2.8645-0.5458-0.01050.1444-0.7407-0.33980.16241.4339-0.2048-0.8696-0.07040.38730.06540.00560.41250.25950.6302-16.7112.9134-29.3245
82.626-1.65822.11032.21113.26172.5752-0.55610.29220.31920.53070.4091-0.6439-0.77940.28540.02130.27340.0666-0.13930.40930.07320.19069.55832.1243-8.3744
92.0794-0.6253-1.77821.68741.8817-0.3063-0.595-0.35040.41020.93330.59430.8065-1.7692-0.486-0.00010.95440.04560.07460.4350.19530.7359-11.5838.2592-2.1259
10-1.44391.3477-0.03450.7993-0.64560.2210.2326-0.31080.78382.05120.28920.2624-1.8626-0.42310.02151.0777-0.1425-0.11530.61690.13240.8137.831819.8449-3.4712
11-1.2378-1.29420.0613.3452-1.6710.6565-0.1029-0.42740.3134-0.54430.2575-0.25890.3431-0.2973-0.01840.2805-0.06810.03980.20360.08630.22892.12663.0309-25.925
123.4366-1.6065-0.32523.7135-2.94393.6842-0.0436-0.0254-0.1130.14730.0861-0.0208-0.24530.0549-0.00060.1048-0.073-0.05550.2365-0.03510.08884.9834-3.3405-19.4744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:70)
2X-RAY DIFFRACTION2(chain A and resid 96:165)
3X-RAY DIFFRACTION3(chain A and resid 166:218)
4X-RAY DIFFRACTION4(chain A and resid 219:265)
5X-RAY DIFFRACTION5(chain A and resid 266:365)
6X-RAY DIFFRACTION6(chain A and resid 378:458)
7X-RAY DIFFRACTION7(chain B and resid 1:70)
8X-RAY DIFFRACTION8(chain B and resid 96:165)
9X-RAY DIFFRACTION9(chain B and resid 166:218)
10X-RAY DIFFRACTION10(chain B and resid 219:265)
11X-RAY DIFFRACTION11(chain B and resid 266:365)
12X-RAY DIFFRACTION12(chain B and resid 378:460)

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