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- PDB-8hgt: Crystal structure of the CYP153A mutant V456A from Marinobacter a... -

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Basic information

Entry
Database: PDB / ID: 8hgt
TitleCrystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / CYP153A
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, 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 / Cytochrome P450
Similarity search - Component
Biological speciesMarinobacter nauticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsJiang, Y. / Tian, X. / Cong, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977104 China
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Enabling Peroxygenase Activity in Cytochrome P450 Monooxygenases by Engineering Hydrogen Peroxide Tunnels.
Authors: Zhao, P. / Kong, F. / Jiang, Y. / Qin, X. / Tian, X. / Cong, Z.
History
DepositionNov 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: 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)55,8672
Polymers55,2511
Non-polymers6161
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-25 kcal/mol
Surface area17360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.120, 103.312, 52.377
Angle α, β, γ (deg.)90.00, 112.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 55250.988 Da / Num. of mol.: 1 / Mutation: V456A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter nauticus (bacteria) / Gene: DET51_1164 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A368UNN3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2M Li2SO4, 0.1M HEPES 7.0, 26% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 25202 / % possible obs: 96.6 % / Redundancy: 3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.064 / Rrim(I) all: 0.112 / Χ2: 0.802 / Net I/σ(I): 10.9
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.428 / Num. unique obs: 2064 / CC1/2: 0.868 / Rpim(I) all: 0.283 / Rrim(I) all: 0.515 / Χ2: 0.447 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FYG

5fyg


Resolution: 2.06→31.38 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1445 5.73 %
Rwork0.2023 --
obs0.2043 25202 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→31.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 43 312 3654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063457
X-RAY DIFFRACTIONf_angle_d0.7344695
X-RAY DIFFRACTIONf_dihedral_angle_d15.7251281
X-RAY DIFFRACTIONf_chiral_restr0.048488
X-RAY DIFFRACTIONf_plane_restr0.004621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.130.31921540.23232305X-RAY DIFFRACTION92
2.13-2.220.26441500.2272411X-RAY DIFFRACTION96
2.22-2.320.29681530.2192469X-RAY DIFFRACTION98
2.32-2.440.26131470.22052471X-RAY DIFFRACTION98
2.44-2.60.22941440.21762466X-RAY DIFFRACTION98
2.6-2.80.22411440.20122453X-RAY DIFFRACTION97
2.8-3.080.2411520.21262413X-RAY DIFFRACTION96
3.08-3.520.22911440.20392332X-RAY DIFFRACTION92
3.52-4.430.21141230.1722131X-RAY DIFFRACTION83
4.43-31.380.2021340.18422306X-RAY DIFFRACTION90

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