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- PDB-9kki: Crystal structure of the CYP153A double mutant L354V/V456G from M... -

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Basic information

Entry
Database: PDB / ID: 9kki
TitleCrystal structure of the CYP153A double mutant L354V/V456G from Marinobacter aquaeolei
ComponentsCytochrome P450
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
LAURIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesMarinobacter nauticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQin, M.M. / Jiang, Y.P. / Cong, Z.Q. / Zhao, P.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the CYP153A double mutant L354V/V456G from Marinobacter aquaeolei at 2.20 Angstroms resolution
Authors: Qin, M.M. / Jiang, Y.P. / Cong, Z.Q. / Zhao, P.X.
History
DepositionNov 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,0796
Polymers110,4462
Non-polymers1,6344
Water8,485471
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0403
Polymers55,2231
Non-polymers8172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0403
Polymers55,2231
Non-polymers8172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.315, 100.490, 223.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cytochrome P450


Mass: 55222.934 Da / Num. of mol.: 2 / Mutation: L354V,V456G
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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.9M Sodium citrate tribasic dihydrate,0.1 M Sodium cacodylate trihydrate pH 6.5

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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: Sep 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→71 Å / Num. obs: 57540 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.073 / Rrim(I) all: 0.186 / Χ2: 0.74 / Net I/σ(I): 5.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.37 / Num. unique obs: 4175 / CC1/2: 0.438 / Rpim(I) all: 0.581 / Rrim(I) all: 1.49 / Χ2: 0.81

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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: 9IXL

9ixl


Resolution: 2.2→55.77 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 1995 3.48 %
Rwork0.2187 --
obs0.2195 57297 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→55.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6643 0 114 471 7228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036971
X-RAY DIFFRACTIONf_angle_d0.6119468
X-RAY DIFFRACTIONf_dihedral_angle_d17.3732602
X-RAY DIFFRACTIONf_chiral_restr0.04987
X-RAY DIFFRACTIONf_plane_restr0.0031254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.32121360.30013843X-RAY DIFFRACTION99
2.26-2.320.29921430.29313927X-RAY DIFFRACTION99
2.32-2.380.32521360.28653901X-RAY DIFFRACTION99
2.38-2.460.29581420.27353915X-RAY DIFFRACTION100
2.46-2.550.31851430.26343903X-RAY DIFFRACTION100
2.55-2.650.30631410.25533928X-RAY DIFFRACTION100
2.65-2.770.29491370.25413903X-RAY DIFFRACTION100
2.77-2.920.26971450.24293923X-RAY DIFFRACTION100
2.92-3.10.27461440.24323969X-RAY DIFFRACTION100
3.1-3.340.22771440.21963960X-RAY DIFFRACTION100
3.34-3.680.24421450.19883963X-RAY DIFFRACTION100
3.68-4.210.18721440.17784008X-RAY DIFFRACTION100
4.21-5.30.18971460.17954017X-RAY DIFFRACTION100
5.3-55.770.21941490.19874142X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -35.6889 Å / Origin y: 10.5966 Å / Origin z: -27.934 Å
111213212223313233
T0.2737 Å20.0358 Å2-0.028 Å2-0.184 Å2-0.0457 Å2--0.1686 Å2
L2.1976 °2-0.2886 °20.1413 °2-0.4197 °2-0.1215 °2--0.4052 °2
S0.0146 Å °-0.1025 Å °-0.0062 Å °0.0227 Å °-0.0225 Å °0.0149 Å °-0.0094 Å °-0.0253 Å °0.0108 Å °
Refinement TLS groupSelection details: all

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