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- PDB-9l7r: Crystal structure of P450cam-F87R mutant complex with (-)-ambroxide -

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Basic information

Entry
Database: PDB / ID: 9l7r
TitleCrystal structure of P450cam-F87R mutant complex with (-)-ambroxide
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
: / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPriestia megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,5706
Polymers104,8652
Non-polymers1,7064
Water4,396244
1
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2853
Polymers52,4321
Non-polymers8532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-25 kcal/mol
Surface area16080 Å2
MethodPISA
2
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2853
Polymers52,4321
Non-polymers8532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-25 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.487, 62.073, 96.128
Angle α, β, γ (deg.)79.24, 80.85, 75.42
Int Tables number1
Space group name H-MP1

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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
Details: Sequence reference for Priestia megaterium (1404) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID P00183.
Source: (gene. exp.) Priestia megaterium (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-A1EI5 / (3~{a}~{R},5~{a}~{S},9~{a}~{S},9~{b}~{R})-3~{a},6,6,9~{a}-tetramethyl-2,4,5,5~{a},7,8,9,9~{b}-octahydro-1~{H}-benzo[e][1]benzofuran / (-)-ambroxide


Mass: 236.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.96 Å3/Da / Density % sol: 37.25 %
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: 2.04→59.36 Å / Num. obs: 47126 / % possible obs: 92.7 % / Redundancy: 1.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.03 / Rrim(I) all: 0.043 / Χ2: 0.89 / Net I/σ(I): 13.4 / Num. measured all: 83673
Reflection shellResolution: 2.04→2.15 Å / % possible obs: 94.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.288 / Num. measured all: 12541 / Num. unique obs: 7019 / CC1/2: 0.848 / Rpim(I) all: 0.288 / Rrim(I) all: 0.407 / Χ2: 0.84 / Net I/σ(I) obs: 2.6

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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: 2.04→29.82 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 2008 4.26 %
Rwork0.2063 --
obs0.2084 47100 92.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6324 0 120 244 6688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056630
X-RAY DIFFRACTIONf_angle_d0.7799050
X-RAY DIFFRACTIONf_dihedral_angle_d9.256916
X-RAY DIFFRACTIONf_chiral_restr0.05968
X-RAY DIFFRACTIONf_plane_restr0.0091188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.35931520.27873252X-RAY DIFFRACTION94
2.09-2.150.27211440.25263335X-RAY DIFFRACTION94
2.15-2.210.29231430.23413251X-RAY DIFFRACTION95
2.21-2.280.30381510.22053290X-RAY DIFFRACTION94
2.28-2.360.27941450.21413213X-RAY DIFFRACTION94
2.36-2.460.26511470.22363277X-RAY DIFFRACTION94
2.46-2.570.3451380.22393246X-RAY DIFFRACTION93
2.57-2.70.28061480.22463225X-RAY DIFFRACTION93
2.7-2.870.33111420.2283192X-RAY DIFFRACTION92
2.87-3.090.23981420.21513186X-RAY DIFFRACTION91
3.09-3.40.26021370.20833147X-RAY DIFFRACTION91
3.4-3.90.24271390.18623139X-RAY DIFFRACTION90
3.9-4.910.21021390.17693133X-RAY DIFFRACTION90
4.91-29.820.23111410.20193206X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1257-0.42910.16641.80460.08454.34130.0025-0.05850.07620.066-0.0902-0.15240.18030.29510.0640.1945-0.0739-0.00040.31970.05610.274-1.5395-25.76739.9883
23.5122-0.97971.67564.7158-0.62025.0940.03420.0283-0.1634-0.26410.0384-0.5502-0.56790.4678-0.06410.3902-0.07280.08420.36070.05480.50993.4774-11.3744-1.065
31.4534-0.1255-0.13051.91280.4313.51190.0290.0954-0.1933-0.0729-0.10320.08940.7984-0.03650.07940.3742-0.00750.00240.29710.04890.2641-4.5829-33.98225.4963
41.43560.6237-0.58822.7754-1.06763.1956-0.04980.226-0.06250.20740.19880.129-0.0054-0.3699-0.12530.1590.0386-0.02760.29670.00550.2246-9.2794-59.515551.385
53.207-0.5415-0.95574.7162-0.20161.7485-0.22080.2407-0.1112-0.221-0.23671.1610.1025-1.03390.25850.52910.0151-0.06911.109-0.28690.6683-14.3514-59.870933.1645
61.60530.096-0.12383.6013-0.72052.49750.0360.10450.21520.64180.0204-0.0534-0.4113-0.0634-0.02030.25310.039-0.00140.23770.00680.2146-6.2635-50.927654.9959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 170 )
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 234 )
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 409 )
4X-RAY DIFFRACTION4chain 'B' and (resid 10 through 170 )
5X-RAY DIFFRACTION5chain 'B' and (resid 171 through 234 )
6X-RAY DIFFRACTION6chain 'B' and (resid 235 through 409 )

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