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- PDB-8x1w: CYP725A4 apo structure -

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Basic information

Entry
Database: PDB / ID: 8x1w
TitleCYP725A4 apo structure
ComponentsTaxadiene 5-alpha hydroxylase
KeywordsBIOSYNTHETIC PROTEIN / P450
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 (ichii)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 9, 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)50,7492
Polymers50,1331
Non-polymers6161
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)196.020, 196.020, 196.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

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Components

#1: Protein Taxadiene 5-alpha hydroxylase


Mass: 50132.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taxus cuspidata (ichii) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WG30, taxadiene 5alpha-hydroxylase
#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.: 89 / 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: 3.13 Å3/Da / Density % sol: 60.7 %
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: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→32.67 Å / Num. obs: 35473 / % possible obs: 94.3 % / Redundancy: 75.5 % / CC1/2: 1 / Net I/σ(I): 45.9
Reflection shellResolution: 2.1→2.175 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3677 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.67 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 1778 5 %
Rwork0.2385 --
obs-35449 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→32.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3536 0 43 89 3668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d14.6281363
X-RAY DIFFRACTIONf_chiral_restr0.056533
X-RAY DIFFRACTIONf_plane_restr0.005632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.33381410.31542715X-RAY DIFFRACTION100
2.15-2.220.37421230.2962707X-RAY DIFFRACTION100
2.22-2.290.30641260.30161893X-RAY DIFFRACTION70
2.29-2.370.39791590.29772698X-RAY DIFFRACTION100
2.37-2.460.29781360.28482738X-RAY DIFFRACTION100
2.58-2.710.35081260.30182310X-RAY DIFFRACTION85
2.71-2.880.37581170.28342785X-RAY DIFFRACTION100
2.88-3.110.29421550.28892739X-RAY DIFFRACTION100
3.11-3.420.2821600.26912745X-RAY DIFFRACTION100
3.42-3.870.26821170.22762081X-RAY DIFFRACTION80
3.93-4.930.22491410.19382761X-RAY DIFFRACTION100

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