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- PDB-9cjg: P450-G9 from Actinokineospora terrae, a non-canonical, serine-lig... -

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Basic information

Entry
Database: PDB / ID: 9cjg
TitleP450-G9 from Actinokineospora terrae, a non-canonical, serine-ligated cytochrome P450 in the ligand-free, closed conformation
ComponentsCytochrome P450-G9
KeywordsOXIDOREDUCTASE / P450 / cytochrome / serine / P411
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 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
1-BUTANOL / FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesActinokineospora terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsIreland, K.A. / Davis, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)R35-GM147557 United States
National Science Foundation (NSF, United States)1937971 United States
CitationJournal: Biorxiv / Year: 2024
Title: Non-Canonical Cytochrome P450 Enzymes in Nature.
Authors: Nguy, A.K.L. / Ireland, K.A. / Kayrouz, C.M. / Caceres, J.C. / Greene, B.L. / Davis, K.M. / Seyedsayamdost, M.R.
History
DepositionJul 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450-G9
B: Cytochrome P450-G9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3328
Polymers88,8582
Non-polymers1,4736
Water8,809489
1
A: Cytochrome P450-G9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2866
Polymers44,4291
Non-polymers8575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450-G9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0462
Polymers44,4291
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.130, 59.650, 233.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cytochrome P450-G9


Mass: 44429.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinokineospora terrae (bacteria) / Gene: SAMN04487818_101238 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1H9KM06, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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 Å3/Da / Density % sol: 38.6 % / Description: Colored rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% (v/v) tacsimate pH 7, 0.7% (v/v) 1-butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 18, 2023
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→57.8 Å / Num. obs: 64200 / % possible obs: 99.3 % / Redundancy: 2 % / Biso Wilson estimate: 23.77 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.03885 / Rpim(I) all: 0.03885 / Rrim(I) all: 0.05494 / Net I/σ(I): 9.59
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3714 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 6334 / CC1/2: 0.68 / CC star: 0.9 / Rpim(I) all: 0.3714 / Rrim(I) all: 0.5253 / % possible all: 99.73

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Processing

Software
NameVersionClassification
MOSFLM7.4.0data reduction
Aimless0.7.7data scaling
PHASERphasing
Coot0.9.8.4model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→57.8 Å / SU ML: 0.2577 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2425 1999 3.12 %
Rwork0.2143 62162 -
obs0.2152 64161 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.59 Å2
Refinement stepCycle: LAST / Resolution: 1.85→57.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5691 0 102 489 6282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00845941
X-RAY DIFFRACTIONf_angle_d0.94368148
X-RAY DIFFRACTIONf_chiral_restr0.0556914
X-RAY DIFFRACTIONf_plane_restr0.01271075
X-RAY DIFFRACTIONf_dihedral_angle_d14.31062085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.35581410.30474396X-RAY DIFFRACTION99.76
1.9-1.950.33971420.28664379X-RAY DIFFRACTION99.76
1.95-20.30941410.26954395X-RAY DIFFRACTION99.58
2-2.070.29561410.25364375X-RAY DIFFRACTION99.54
2.07-2.140.28291420.2374418X-RAY DIFFRACTION99.41
2.14-2.230.26311410.22844380X-RAY DIFFRACTION99.47
2.23-2.330.27361420.22484406X-RAY DIFFRACTION99.34
2.33-2.450.26131410.22434400X-RAY DIFFRACTION99.52
2.45-2.610.25881410.22444408X-RAY DIFFRACTION98.93
2.61-2.810.27721430.21244453X-RAY DIFFRACTION99.31
2.81-3.090.2491430.2144410X-RAY DIFFRACTION98.53
3.09-3.540.2431420.19764443X-RAY DIFFRACTION98.12
3.54-4.460.19091450.17794525X-RAY DIFFRACTION99.11
4.46-57.80.19521540.20354774X-RAY DIFFRACTION99.9

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