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- PDB-9u5y: Crystal structure of cytochrome P450 mutant-T288G S289Q G290E T29... -

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Basic information

Entry
Database: PDB / ID: 9u5y
TitleCrystal structure of cytochrome P450 mutant-T288G S289Q G290E T291I of CYP161H12 from Amycolatopsis pretoriensis
ComponentsPentalenolactone synthase
KeywordsBIOSYNTHETIC PROTEIN / CYP / P450 / pentaclyclic triterpenoids / oxidation / cytochrome / Amycolatopsis / pretoriensis / OXIDOREDUCTASE
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesAmycolatopsis pretoriensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDong, L.B. / Zhang, X.W. / Wang, Y.X. / Pan, X.M. / Liu, C.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073746 China
CitationJournal: To Be Published
Title: Reshape the Active Pocket of ApPT for Divergent Synthesis of Pentacyclic Triterpenoids with Expanded Chemical Space in B-Ring.
Authors: Zhang, X.W. / Wang, Y.X. / Dong, L.B.
History
DepositionMar 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pentalenolactone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1962
Polymers43,5791
Non-polymers6161
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, According to gel filtration chromatography analysis, the protein is monomer in solution state.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.940, 74.940, 141.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Pentalenolactone synthase


Mass: 43579.035 Da / Num. of mol.: 1 / Mutation: T288G S289Q G290E T291I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis pretoriensis (bacteria) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES monohydrate pH 6.0 22% Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→19.99 Å / Num. obs: 18685 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.051 / Rrim(I) all: 0.137 / Χ2: 0.98 / Net I/σ(I): 12.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 3 / Num. unique obs: 1773 / CC1/2: 0.839 / Rpim(I) all: 0.36 / Rrim(I) all: 0.922 / Χ2: 0.89

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.99 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 1862 10 %
Rwork0.206 --
obs0.2094 18620 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 75 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113005
X-RAY DIFFRACTIONf_angle_d1.2074085
X-RAY DIFFRACTIONf_dihedral_angle_d16.1091137
X-RAY DIFFRACTIONf_chiral_restr0.058447
X-RAY DIFFRACTIONf_plane_restr0.02566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.32431410.25851271X-RAY DIFFRACTION100
2.36-2.430.28211390.24631250X-RAY DIFFRACTION100
2.43-2.510.31711390.24521259X-RAY DIFFRACTION100
2.51-2.60.27911410.23551259X-RAY DIFFRACTION100
2.6-2.70.29031400.23261260X-RAY DIFFRACTION100
2.7-2.830.27261400.23271269X-RAY DIFFRACTION100
2.83-2.970.27861430.24511281X-RAY DIFFRACTION100
2.97-3.160.24771420.23691279X-RAY DIFFRACTION100
3.16-3.40.2661440.21481292X-RAY DIFFRACTION100
3.4-3.740.2241430.19661289X-RAY DIFFRACTION100
3.74-4.280.21311440.16951296X-RAY DIFFRACTION100
4.28-5.370.19611490.17351341X-RAY DIFFRACTION100
5.38-19.990.21751570.20651412X-RAY DIFFRACTION100

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