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

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Basic information

Entry
Database: PDB / ID: 8hgd
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 / METHANOL / Cytochrome P450
Similarity search - Component
Biological speciesMarinobacter nauticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsJiang, Y. / Cong, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977104 China
CitationJournal: To Be Published
Title: Crystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei
Authors: Jiang, Y. / Cong, Z.
History
DepositionNov 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9924
Polymers55,2511
Non-polymers7413
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-27 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.150, 103.369, 52.489
Angle α, β, γ (deg.)90.00, 112.28, 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: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M (NH4)2SO4, 0.1 M 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: 1.53→50 Å / Num. obs: 65017 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Χ2: 0.932 / Net I/σ(I): 23.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Χ2% possible all
1.53-1.562.60.21931330.9160.71996.1
1.56-1.582.70.19532410.9360.75398.8
1.58-1.622.90.1832220.9490.80699.3
1.62-1.6530.16832700.9560.89699.9
1.65-1.683.40.1632430.9670.97199.9
1.68-1.723.20.14832540.9631.035100
1.72-1.773.40.13732940.9681.16699.8
1.77-1.813.40.11632380.9781.10299.7
1.81-1.873.30.10532710.9791.12399.8
1.87-1.933.20.09132420.9821.15699.7
1.93-23.40.08632520.9851.18199.3
2-2.083.30.07432540.9881.20199.5
2.08-2.173.40.06532430.9911.09699.6
2.17-2.293.40.0632480.9921.08199.3
2.29-2.433.20.05332670.9930.97499.7
2.43-2.623.40.04932860.9940.90399.9
2.62-2.883.50.04432520.9950.79899.9
2.88-3.33.40.03732660.9960.64699.2
3.3-4.153.40.0332440.9970.52198.4
4.15-503.30.02732970.9970.37498.5

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Processing

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

5fyg


Resolution: 1.53→31.38 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1846 1997 3.12 %
Rwork0.1692 --
obs0.1697 64008 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→31.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 51 531 3859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073429
X-RAY DIFFRACTIONf_angle_d0.8984661
X-RAY DIFFRACTIONf_dihedral_angle_d16.1711266
X-RAY DIFFRACTIONf_chiral_restr0.057484
X-RAY DIFFRACTIONf_plane_restr0.006620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.23851210.2183652X-RAY DIFFRACTION81
1.57-1.610.21571350.18744224X-RAY DIFFRACTION94
1.61-1.660.21061450.18174466X-RAY DIFFRACTION99
1.66-1.710.19361440.17724537X-RAY DIFFRACTION100
1.71-1.770.19491460.17924507X-RAY DIFFRACTION100
1.77-1.840.20071480.17494517X-RAY DIFFRACTION100
1.84-1.930.17851440.1714511X-RAY DIFFRACTION100
1.93-2.030.18081470.17254492X-RAY DIFFRACTION99
2.03-2.160.18261430.16644495X-RAY DIFFRACTION100
2.16-2.320.2061430.16454536X-RAY DIFFRACTION99
2.32-2.560.20351500.17384497X-RAY DIFFRACTION100
2.56-2.930.19441440.17224540X-RAY DIFFRACTION100
2.93-3.690.15681440.16564508X-RAY DIFFRACTION99
3.69-31.380.16361430.15364529X-RAY DIFFRACTION98

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