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- PDB-9kg5: Crystal structure of the CYP154C5 F92A/R114A/T248D/E282A variant ... -

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Basic information

Entry
Database: PDB / ID: 9kg5
TitleCrystal structure of the CYP154C5 F92A/R114A/T248D/E282A variant from Nocardia farcinica
ComponentsCytochrome P450 monooxygenase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Monooxygenase / Metalloprotein
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 / : / TESTOSTERONE / Cytochrome P450 monooxygenase
Similarity search - Component
Biological speciesNocardia farcinica IFM 10152 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsQin, M.M. / Fan, S.X. / Cong, Z.Q. / Jiang, Y.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2025
Title: Semirationally Engineering an Efficient P450 Peroxygenase for Regio- and Enantioselective Hydroxylation of Steroids
Authors: Fan, S. / Qin, M. / Wang, Q. / Jiang, Y. / Cong, Z.
History
DepositionNov 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cytochrome P450 monooxygenase
A: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,98216
Polymers94,3692
Non-polymers2,61314
Water13,637757
1
B: Cytochrome P450 monooxygenase
A: Cytochrome P450 monooxygenase
hetero molecules

B: Cytochrome P450 monooxygenase
A: Cytochrome P450 monooxygenase
hetero molecules

B: Cytochrome P450 monooxygenase
A: Cytochrome P450 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,94748
Polymers283,1086
Non-polymers7,83942
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area24700 Å2
ΔGint-397 kcal/mol
Surface area89130 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-111 kcal/mol
Surface area31350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.360, 103.360, 218.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Cytochrome P450 monooxygenase


Mass: 47184.699 Da / Num. of mol.: 2 / Mutation: F92A,R114A,T248D,E282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia farcinica IFM 10152 (bacteria)
Gene: NFA_53110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5YNS8

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Non-polymers , 7 types, 771 molecules

#2: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 757 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 205mM MgCl2,5mM CdCl2,100mM HEPES PH 7.5, 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→27.61 Å / Num. obs: 86129 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.072 / Rrim(I) all: 0.162 / Χ2: 0.93 / Net I/σ(I): 7 / Num. measured all: 440282
Reflection shellResolution: 1.76→1.81 Å / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.999 / Num. measured all: 32101 / Num. unique obs: 6429 / CC1/2: 0.603 / Rpim(I) all: 0.497 / Rrim(I) all: 1.117 / Χ2: 0.7 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9JS9

9js9


Resolution: 1.85→24.67 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 1718 2.32 %
Rwork0.1881 --
obs0.1884 74031 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6135 0 143 757 7035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036476
X-RAY DIFFRACTIONf_angle_d0.6388903
X-RAY DIFFRACTIONf_dihedral_angle_d17.4472314
X-RAY DIFFRACTIONf_chiral_restr0.0421048
X-RAY DIFFRACTIONf_plane_restr0.0041135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.33241380.26975970X-RAY DIFFRACTION100
1.9-1.970.26141460.26266068X-RAY DIFFRACTION100
1.97-2.040.24541430.22366010X-RAY DIFFRACTION100
2.04-2.120.23541420.21266041X-RAY DIFFRACTION100
2.12-2.210.22231430.21166025X-RAY DIFFRACTION100
2.21-2.330.25731400.20186001X-RAY DIFFRACTION100
2.33-2.480.20461450.20786039X-RAY DIFFRACTION100
2.48-2.670.22471420.19956020X-RAY DIFFRACTION100
2.67-2.940.21461480.20436059X-RAY DIFFRACTION100
2.94-3.360.23381440.18916029X-RAY DIFFRACTION100
3.36-4.230.1751400.16056027X-RAY DIFFRACTION100
4.23-24.670.14781470.16086024X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 26.7519 Å / Origin y: -15.5058 Å / Origin z: 4.2794 Å
111213212223313233
T0.1544 Å20.0248 Å20.0053 Å2-0.1909 Å2-0.0073 Å2--0.2016 Å2
L0.1563 °20.0656 °2-0.0504 °2-0.2282 °2-0.0521 °2--0.4838 °2
S-0.0025 Å °0.0144 Å °0.016 Å °0.0112 Å °0.005 Å °0.0288 Å °-0.0205 Å °-0.0666 Å °0 Å °
Refinement TLS groupSelection details: all

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