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

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Basic information

Entry
Database: PDB / ID: 8hge
TitleCrystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei in complex with 12-hydroxydodecanoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / CYP153A / Complex
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
12-HYDROXYDODECANOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / 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 in complex with 12-hydroxydodecanoic acid
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)56,0843
Polymers55,2511
Non-polymers8332
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-24 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.522, 103.568, 52.738
Angle α, β, γ (deg.)90.00, 112.19, 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-12H / 12-HYDROXYDODECANOIC ACID


Mass: 216.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Li2SO4, 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: 63827 / % possible obs: 95.6 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Rrim(I) all: 0.057 / Χ2: 0.894 / Net I/σ(I): 19.9
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.132 / Num. unique obs: 2949 / CC1/2: 0.964 / Rpim(I) all: 0.097 / Rrim(I) all: 0.165 / Χ2: 0.794 / % possible all: 87.9

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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→31.54 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1871 2006 3.15 %
Rwork0.1599 --
obs0.1608 63741 95.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 58 549 3940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123485
X-RAY DIFFRACTIONf_angle_d1.2224728
X-RAY DIFFRACTIONf_dihedral_angle_d17.1211298
X-RAY DIFFRACTIONf_chiral_restr0.072490
X-RAY DIFFRACTIONf_plane_restr0.009625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.21711240.2083950X-RAY DIFFRACTION85
1.57-1.610.17971370.15444226X-RAY DIFFRACTION91
1.61-1.660.19491590.15394382X-RAY DIFFRACTION95
1.66-1.710.19531320.1524421X-RAY DIFFRACTION96
1.71-1.770.19851460.15424397X-RAY DIFFRACTION96
1.77-1.840.17541550.15554437X-RAY DIFFRACTION96
1.84-1.920.16781490.15674449X-RAY DIFFRACTION96
1.92-2.030.19751460.16264483X-RAY DIFFRACTION96
2.03-2.150.20581400.15834432X-RAY DIFFRACTION97
2.15-2.320.18531350.15614499X-RAY DIFFRACTION97
2.32-2.550.16041490.15964509X-RAY DIFFRACTION97
2.55-2.920.1671410.16494553X-RAY DIFFRACTION98
2.92-3.680.20521480.16644533X-RAY DIFFRACTION97
3.68-31.540.18841450.15314464X-RAY DIFFRACTION95

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