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- PDB-7wyg: Crystal structure of P450BSbeta-L78I/Q85H/G290I variant in comple... -

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Basic information

Entry
Database: PDB / ID: 7wyg
TitleCrystal structure of P450BSbeta-L78I/Q85H/G290I variant in complex with palmitic acid.
ComponentsCytochrome P450 152A1
KeywordsOXIDOREDUCTASE / cytochrome P450
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group I / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PALMITOLEIC ACID / DI(HYDROXYETHYL)ETHER / Cytochrome P450 152A1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, F. / He, C. / Wang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171410 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Biocatalytic Enantioselective beta-Hydroxylation of Unactivated C-H Bonds in Aliphatic Carboxylic Acids.
Authors: Zhang, K. / Yu, A. / Chu, X. / Li, F. / Liu, J. / Liu, L. / Bai, W.J. / He, C. / Wang, X.
History
DepositionFeb 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 152A1
B: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,62418
Polymers96,7732
Non-polymers2,85216
Water8,035446
1
A: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,13012
Polymers48,3861
Non-polymers1,74411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-11 kcal/mol
Surface area17720 Å2
MethodPISA
2
B: Cytochrome P450 152A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4946
Polymers48,3861
Non-polymers1,1075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-19 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.646, 125.646, 145.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

21A-846-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450 152A1


Mass: 48386.320 Da / Num. of mol.: 2 / Mutation: L78I, Q85H, G290I valiant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_1418 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164W6Q6

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Non-polymers , 5 types, 462 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-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.44 Å3/Da / Density % sol: 64.19 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 38 % PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→57.7 Å / Num. obs: 81571 / % possible obs: 90.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 37.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 20.9 / Num. measured all: 506270 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.043.30.6231572847300.6740.3870.741.897.5
10.39-57.75.50.02139557140.9990.0090.02262.997.8

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.19-4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IZO

1izo


Resolution: 2→50.98 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 4026 4.94 %
Rwork0.1743 77523 -
obs0.1759 81549 90.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.74 Å2 / Biso mean: 43.03 Å2 / Biso min: 23.71 Å2
Refinement stepCycle: final / Resolution: 2→50.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 194 446 7264
Biso mean--42.06 44.87 -
Num. residues----816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.30021610.2552810297197
2.02-2.050.28091380.24642871300998
2.05-2.070.3155580.254970376125
2.07-2.10.26371300.2412508263888
2.1-2.130.25211620.201429653127100
2.13-2.160.22071860.199128673053100
2.16-2.190.20721630.199729023065100
2.19-2.230.24081640.19529123076100
2.23-2.260.2849590.21391250130942
2.26-2.30.25371700.179928893059100
2.3-2.340.19661470.169829543101100
2.34-2.390.18371280.165829593087100
2.39-2.440.1981390.17429583097100
2.44-2.490.20321640.168529103074100
2.49-2.550.20241590.173729303089100
2.55-2.610.21361680.176329553123100
2.61-2.640.2183660.18981300136697
2.69-2.760.21231280.19422725285397
2.76-2.850.24651470.204429563103100
2.85-2.950.26361620.197929233085100
2.95-3.070.23031330.195229733106100
3.07-3.210.21411500.189429813131100
3.21-3.380.23511550.188629593114100
3.38-3.590.20391010.16572088218970
3.59-3.870.19071280.16082481260984
3.91-4.260.17191270.14632582270999
4.26-4.880.18211570.143629963153100
4.88-6.140.211380.163630543192100
6.14-50.980.17961380.16653162330099
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)
10.8108-0.21010.2361.228-0.15781.2457-0.08950.03160.0701-0.11220.03450.1543-0.057-0.15170.05160.3394-0.0299-0.07370.3823-0.04130.307133.0172-38.844121.2023
21.0720.14-0.05481.11670.25981.0783-0.01320.0288-0.05660.0163-0.08590.19150.0562-0.1110.08940.273-0.00530.0110.2502-0.0520.327642.3566-14.657461.6451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 6 through 416)B6 - 416
2X-RAY DIFFRACTION2(chain 'A' and resid 12 through 416)A12 - 416

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