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- PDB-8q6y: Crystal structure of Cytochrome P450 GymB5 from Streptomyces katr... -

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Basic information

Entry
Database: PDB / ID: 8q6y
TitleCrystal structure of Cytochrome P450 GymB5 from Streptomyces katrae in complex with cYY and Hypoxanthine
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Nucleobase transferase / Cytochrome P450 / Mycocyclosin synthetase / prism-like fold
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HYPOXANTHINE / Chem-YTT / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces katrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsFreytag, J. / Mueller, J.M. / 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,30111
Polymers90,1472
Non-polymers2,1549
Water9,980554
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2155
Polymers45,0741
Non-polymers1,1414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0866
Polymers45,0741
Non-polymers1,0135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.830, 95.482, 79.451
Angle α, β, γ (deg.)90.00, 108.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450


Mass: 45073.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces katrae (bacteria) / Gene: VR44_17910 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F4JF04

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Non-polymers , 5 types, 563 molecules

#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-YTT / (3S,6S)-3,6-bis(4-hydroxybenzyl)piperazine-2,5-dione / cyclo(tyrosyl-tyrosyl) / Cyclo(tyr-tyr)


Mass: 326.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H4N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate, 20 mM potassium sodium tartrate, 20 mM sodium oxamate, 13% MPD, 13% PEG 1000, 13% PEG3350, 100 mM BIS-Tris pH 8.7, 1.25% DMSO

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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: 1.8→49.02 Å / Num. obs: 83878 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 0.99 / Rrim(I) all: 0.13 / Net I/σ(I): 10.3
Reflection shellResolution: 1.81→1.92 Å / Num. unique obs: 13448 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→41.72 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.786 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21633 1678 2 %RANDOM
Rwork0.18494 ---
obs0.18557 82200 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0.47 Å2
2---1.77 Å20 Å2
3---1.4 Å2
Refinement stepCycle: 1 / Resolution: 1.81→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5922 0 152 554 6628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136277
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175841
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.6648578
X-RAY DIFFRACTIONr_angle_other_deg1.431.57913501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.02421.575292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91415980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2131541
X-RAY DIFFRACTIONr_chiral_restr0.0880.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027091
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021308
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_it1.31.8753131
X-RAY DIFFRACTIONr_mcbond_other1.2991.8733130
X-RAY DIFFRACTIONr_mcangle_it2.0232.0893919
X-RAY DIFFRACTIONr_mcangle_other2.0232.0913920
X-RAY DIFFRACTIONr_scbond_it2.4662.7553146
X-RAY DIFFRACTIONr_scbond_other2.4672.7593147
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4112.9014660
X-RAY DIFFRACTIONr_long_range_B_refined7.16511.2577278
X-RAY DIFFRACTIONr_long_range_B_other7.13710.4537145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.854 Å
RfactorNum. reflection% reflection
Rfree0.377 122 -
Rwork0.381 5981 -
obs--98.64 %
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)
12.6656-0.54080.19993.160.25491.83990.021-0.0363-0.05920.012-0.03560.43070.0892-0.3520.01460.3482-0.03230.00910.3397-0.06740.1416-7.18-4.240211.6989
20.7745-0.40.01490.8739-0.30621.0250.04910.07680.1533-0.0996-0.0998-0.0723-0.07280.03430.05070.4733-0.00590.04080.2297-0.00860.049916.96435.07278.2866
30.8334-0.3240.36611.1321-0.20691.21040.05060.0645-0.0318-0.1014-0.07590.05470.0759-0.08880.02520.4104-0.00380.03960.2218-0.01970.009810.5373-3.32999.0889
41.3027-0.6046-0.47323.78440.27653.3231-0.0242-0.0694-0.11170.285-0.0194-0.16890.28290.18730.04350.4752-0.02950.0540.16740.00950.039811.8735-3.97651.4993
52.7039-1.46261.88592.2095-1.5712.72750.0649-0.0020.03490.0046-0.0782-0.2953-0.03820.23460.01320.4364-0.02750.05940.2116-0.02090.076725.812416.487836.7751
60.53970.027-0.22081.48390.33530.9991-0.0022-0.08550.00070.1626-0.0079-0.05770.05860.02750.010.4265-0.02080.0290.1889-0.0030.005915.86778.646444.1434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 74
2X-RAY DIFFRACTION2A75 - 175
3X-RAY DIFFRACTION3A176 - 398
4X-RAY DIFFRACTION4B10 - 95
5X-RAY DIFFRACTION5B96 - 163
6X-RAY DIFFRACTION6B164 - 397

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