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- PDB-8ws4: Crystal structure of the CYP199A4 mutant F182A in complex with 4-... -

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Basic information

Entry
Database: PDB / ID: 8ws4
TitleCrystal structure of the CYP199A4 mutant F182A in complex with 4-methoxybenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / CYP199A4 / Complex
Function / homologyACETATE ION / 4-METHOXYBENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsJiang, Y. / Cong, Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977104 China
National Natural Science Foundation of China (NSFC)32371311 China
National Natural Science Foundation of China (NSFC)22207112 China
CitationJournal: Chem Sci / Year: 2024
Title: Crucial gating residues govern the enhancement of peroxygenase activity in an engineered cytochrome P450 O -demethylase.
Authors: Zhao, P. / Jiang, Y. / Wang, Q. / Chen, J. / Yao, F. / Cong, Z.
History
DepositionOct 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5984
Polymers45,7711
Non-polymers8283
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-23 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.674, 51.829, 78.959
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 45770.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic)
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M MgAc, 0.1 M Bis-tris 5.5, 27% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.41→31.38 Å / Num. obs: 65621 / % possible obs: 94.4 % / Redundancy: 2.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.034 / Rrim(I) all: 0.062 / Χ2: 0.63 / Net I/σ(I): 7.4 / Num. measured all: 185834
Reflection shellResolution: 1.41→1.45 Å / % possible obs: 62.1 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.323 / Num. measured all: 5142 / Num. unique obs: 3135 / CC1/2: 0.809 / Rpim(I) all: 0.293 / Rrim(I) all: 0.438 / Χ2: 0.43 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→30.38 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1759 1663 3.07 %
Rwork0.1548 --
obs0.1554 54219 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 58 481 3545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063195
X-RAY DIFFRACTIONf_angle_d0.9044378
X-RAY DIFFRACTIONf_dihedral_angle_d23.2541180
X-RAY DIFFRACTIONf_chiral_restr0.052478
X-RAY DIFFRACTIONf_plane_restr0.006585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.580.23261370.20694261X-RAY DIFFRACTION98
1.58-1.630.23611380.19854359X-RAY DIFFRACTION100
1.63-1.680.19331310.17924367X-RAY DIFFRACTION100
1.68-1.750.22311520.17534364X-RAY DIFFRACTION99
1.75-1.830.18081280.16644350X-RAY DIFFRACTION100
1.83-1.930.1831370.15884385X-RAY DIFFRACTION99
1.93-2.050.20891380.16164369X-RAY DIFFRACTION100
2.05-2.210.18181390.15414379X-RAY DIFFRACTION99
2.21-2.430.18241350.1514373X-RAY DIFFRACTION100
2.43-2.780.20221410.15594408X-RAY DIFFRACTION99
2.78-3.50.16131440.1484422X-RAY DIFFRACTION100
3.5-30.380.13661430.1374519X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.0856 Å / Origin y: -6.9336 Å / Origin z: 19.3012 Å
111213212223313233
T0.0738 Å20.0033 Å2-0.0039 Å2-0.0791 Å20.0017 Å2--0.0674 Å2
L0.2236 °2-0.0211 °2-0.0417 °2-0.8299 °20.1445 °2--0.3844 °2
S-0.0077 Å °-0.0143 Å °0.0009 Å °-0.1025 Å °0.0178 Å °-0.0175 Å °0.0093 Å °0.002 Å °0.0005 Å °
Refinement TLS groupSelection details: all

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