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- PDB-8x3e: CYP725A4-Taxa-4,11-diene complex -

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Basic information

Entry
Database: PDB / ID: 8x3e
TitleCYP725A4-Taxa-4,11-diene complex
ComponentsTaxadiene 5-alpha hydroxylase
KeywordsBIOSYNTHETIC PROTEIN / Complex
Function / homology
Function and homology information


taxadiene 5alpha-hydroxylase / taxadiene 5-alpha-hydroxylase activity / paclitaxel biosynthetic process / sterol metabolic process / iron ion binding / heme binding / membrane
Similarity search - Function
Cytochrome P450, E-class, group I / 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 / Taxadiene 5-alpha hydroxylase
Similarity search - Component
Biological speciesTaxus cuspidata (Japanese yew)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChang, Z. / Wang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2024
Title: Unraveling the Catalytic Mechanism of Taxadiene-5alpha-hydroxylase from Crystallography and Computational Analyses.
Authors: Song, X. / Wang, Q. / Zhu, X. / Fang, W. / Liu, X. / Shi, C. / Chang, Z. / Jiang, H. / Wang, B.
History
DepositionNov 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Taxadiene 5-alpha hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2853
Polymers48,3961
Non-polymers8892
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)196.824, 196.824, 196.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Taxadiene 5-alpha hydroxylase


Mass: 48395.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taxus cuspidata (Japanese yew) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WG30, taxadiene 5alpha-hydroxylase
#2: Chemical ChemComp-A1L3H / (1~{R},3~{R},8~{R})-4,8,12,15,15-pentamethyltricyclo[9.3.1.0^{3,8}]pentadeca-4,11-diene


Mass: 272.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 1.6M sodium citrate, pH6.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→28.41 Å / Num. obs: 22650 / % possible obs: 99.31 % / Redundancy: 76.1 % / CC1/2: 0.998 / Net I/σ(I): 35.6
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 2228 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.41 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3109 1172 -
Rwork0.2974 --
obs-22647 99.7 %
Refinement stepCycle: LAST / Resolution: 2.5→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 0 73 3548

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