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- PDB-8q6z: Crystal structure of Cytochrome P450 GymB1 from Streptomyces flav... -

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Basic information

Entry
Database: PDB / ID: 8q6z
TitleCrystal structure of Cytochrome P450 GymB1 from Streptomyces flavidovirens
ComponentsGymB1
KeywordsOXIDOREDUCTASE / Nucleobase transferase / Cytochrome P450 / Mycocyclosin synthetase / prism-like fold
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesStreptomyces flavidovirens DSM 40150 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsFreytag, J. / Kelm, T. / Stehle, T. / Zocher, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)TRR261 Germany
CitationJournal: Chemcatchem / Year: 2024
Title: Intramolecular Coupling and Nucleobase Transfer - How Cytochrome P450 Enzymes GymBx Establish Their Chemoselectivity
Authors: Freytag, J. / Martin, A. / Muller, J.C. / Kelm, T. / Stehle, T. / Li, S.M. / Zocher, G.
History
DepositionAug 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GymB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9643
Polymers43,2561
Non-polymers7092
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-27 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.076, 98.076, 94.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein GymB1


Mass: 43255.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces flavidovirens DSM 40150 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 16% PEG 8000, 20% glycerol, 40 mM KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→49.04 Å / Num. obs: 38173 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.99 / Rrim(I) all: 0.1 / Net I/σ(I): 15.4
Reflection shellResolution: 1.96→2.08 Å / Num. unique obs: 6065 / CC1/2: 0.59 / Rrim(I) all: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→49.04 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 8.199 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21434 1909 5 %RANDOM
Rwork0.18531 ---
obs0.18673 36263 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.184 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å2-0 Å2
2---0.53 Å20 Å2
3---1.72 Å2
Refinement stepCycle: 1 / Resolution: 1.96→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 49 253 3288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133110
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172959
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.6694256
X-RAY DIFFRACTIONr_angle_other_deg1.3281.5856829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.25320.987152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55915490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.041526
X-RAY DIFFRACTIONr_chiral_restr0.0740.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02644
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1023.0231559
X-RAY DIFFRACTIONr_mcbond_other1.0943.0231558
X-RAY DIFFRACTIONr_mcangle_it1.7234.5291947
X-RAY DIFFRACTIONr_mcangle_other1.7224.5291948
X-RAY DIFFRACTIONr_scbond_it1.3883.2761551
X-RAY DIFFRACTIONr_scbond_other1.3883.2781552
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2424.8512310
X-RAY DIFFRACTIONr_long_range_B_refined4.90437.5373513
X-RAY DIFFRACTIONr_long_range_B_other4.83237.063466
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.008 Å
RfactorNum. reflection% reflection
Rfree0.389 138 -
Rwork0.356 2613 -
obs--98.67 %
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)
12.95972.09540.35263.41580.0313.26080.0302-0.0885-0.3972-0.04510.0726-0.25760.3420.1654-0.10280.08660.0031-0.03730.02610.01330.1665-25.79347.09096.0255
24.30220.89760.36881.7725-0.16782.2362-0.06860.122-0.1763-0.12050.03080.29470.0836-0.28660.03780.0689-0.0394-0.00850.0566-0.02230.1309-33.102933.95660.7872
32.3545-0.1989-1.28431.19690.43043.41390.04820.13030.0277-0.133-0.04850.2051-0.1346-0.38990.00030.0537-0.0221-0.01280.0839-0.01720.1159-35.057230.42866.699
41.38131.1953-0.10572.5415-0.8061.3925-0.06410.1911-0.1692-0.30710.1259-0.07040.1760.0575-0.06180.1114-0.04850.01270.069-0.0540.1226-25.129217.4349-4.2872
54.5353.6259-1.82396.0596-1.7221.5566-0.06240.1165-0.1985-0.2031-0.0404-0.01210.15820.11920.10280.0553-0.01030.00180.0902-0.01270.0531-15.035327.79658.4384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 80
2X-RAY DIFFRACTION2A81 - 143
3X-RAY DIFFRACTION3A144 - 265
4X-RAY DIFFRACTION4A266 - 371
5X-RAY DIFFRACTION5A372 - 398

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