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- PDB-9l7q: Crystal structure of P450cam-F87R mutant -

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Basic information

Entry
Database: PDB / ID: 9l7q
TitleCrystal structure of P450cam-F87R mutant
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / cytochrome p450
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsDong, S. / Feng, Y.G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071266 China
National Natural Science Foundation of China (NSFC)32171203 China
CitationJournal: To Be Published
Title: Crystal structure of P450cam-F87R mutant
Authors: Dong, S. / Feng, Y.G.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Camphor 5-monooxygenase
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2166
Polymers104,8652
Non-polymers1,3514
Water10,467581
1
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1083
Polymers52,4321
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area16180 Å2
MethodPISA
2
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1083
Polymers52,4321
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-24 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.059, 100.582, 72.952
Angle α, β, γ (deg.)90.00, 109.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Camphor 5-monooxygenase / Cytochrome P450-cam / Cytochrome P450cam


Mass: 52432.281 Da / Num. of mol.: 2 / Mutation: F88R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00183, camphor 5-monooxygenase
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 1.91 Å3/Da / Density % sol: 35.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.04 M citric acid,0.06 M bis-tris, pH6.4, 24% 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 PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→56.69 Å / Num. obs: 61407 / % possible obs: 87.5 % / Redundancy: 3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Χ2: 0.86 / Net I/σ(I): 12.6 / Num. measured all: 185987
Reflection shellResolution: 1.82→1.92 Å / % possible obs: 53.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.447 / Num. measured all: 14340 / Num. unique obs: 5413 / CC1/2: 0.847 / Rpim(I) all: 0.318 / Rrim(I) all: 0.552 / Χ2: 0.7 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→28.65 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 1997 3.26 %
Rwork0.1797 --
obs0.181 61290 87.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 94 581 7091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086676
X-RAY DIFFRACTIONf_angle_d0.9819098
X-RAY DIFFRACTIONf_dihedral_angle_d8.029898
X-RAY DIFFRACTIONf_chiral_restr0.058976
X-RAY DIFFRACTIONf_plane_restr0.0111202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.40181610.35064747X-RAY DIFFRACTION99
1.87-1.90.5343190.6383474X-RAY DIFFRACTION14
1.93-1.980.4518600.34951807X-RAY DIFFRACTION43
1.98-2.040.25591660.21634777X-RAY DIFFRACTION99
2.04-2.110.24681540.20464832X-RAY DIFFRACTION99
2.11-2.20.23051690.19414746X-RAY DIFFRACTION99
2.2-2.30.26931670.19624808X-RAY DIFFRACTION99
2.3-2.420.28241640.18514790X-RAY DIFFRACTION99
2.42-2.570.23181570.18394797X-RAY DIFFRACTION99
2.57-2.770.22681590.17834819X-RAY DIFFRACTION99
2.77-3.050.23061690.17294790X-RAY DIFFRACTION99
3.05-3.490.21791660.16364767X-RAY DIFFRACTION99
3.49-4.390.15771400.1434299X-RAY DIFFRACTION88
4.39-28.650.15931460.16754840X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 19.5651 Å / Origin y: -20.6018 Å / Origin z: 19.4469 Å
111213212223313233
T0.1435 Å20.0178 Å2-0.0043 Å2-0.1478 Å2-0.0064 Å2--0.1566 Å2
L0.0909 °20.0176 °20.0011 °2-0.1756 °20.1042 °2--0.0822 °2
S-0.0041 Å °-0.0156 Å °-0.0076 Å °0.0113 Å °-0.0053 Å °0.0193 Å °0.005 Å °0.0306 Å °-0 Å °
Refinement TLS groupSelection details: all

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