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- PDB-7wpy: AndA_M119A_N121V variant -

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Basic information

Entry
Database: PDB / ID: 7wpy
TitleAndA_M119A_N121V variant
ComponentsDioxygenase andA
KeywordsOXIDOREDUCTASE / non heme iron 2-oxoglutarate dependent dioxygenase / meroterpenoid
Function / homologyOxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / terpenoid biosynthetic process / dioxygenase activity / metal ion binding / : / Dioxygenase andA
Function and homology information
Biological speciesAspergillus stellatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMori, T. / Chen, H. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: AndA_M119A_N121V variant
Authors: Mori, T. / Chen, H. / Abe, I.
History
DepositionJan 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dioxygenase andA
B: Dioxygenase andA
C: Dioxygenase andA
D: Dioxygenase andA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,7888
Polymers134,5654
Non-polymers2234
Water6,756375
1
A: Dioxygenase andA
C: Dioxygenase andA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3944
Polymers67,2822
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-43 kcal/mol
Surface area21400 Å2
MethodPISA
2
B: Dioxygenase andA
hetero molecules

D: Dioxygenase andA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3944
Polymers67,2822
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area3470 Å2
ΔGint-42 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.517, 73.763, 97.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Dioxygenase andA / Anditomin synthesis protein A


Mass: 33641.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus stellatus (mold) / Gene: andA / Production host: Escherichia coli (E. coli)
References: UniProt: A0A097ZPD5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.13 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 28% PEG3350, 0.2 M LiCl, 5% DMF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.74 Å / Num. obs: 48937 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.3
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4453 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZM2

5zm2


Resolution: 2.25→40.45 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8985
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2415 2017 4.13 %
Rwork0.1879 46867 -
obs0.1901 48884 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.45 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8234 0 4 375 8613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078410
X-RAY DIFFRACTIONf_angle_d0.898411427
X-RAY DIFFRACTIONf_chiral_restr0.05161274
X-RAY DIFFRACTIONf_plane_restr0.00831519
X-RAY DIFFRACTIONf_dihedral_angle_d6.24421145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.28411520.22953292X-RAY DIFFRACTION99.97
2.31-2.370.26691360.2173340X-RAY DIFFRACTION99.97
2.37-2.440.28651390.23193304X-RAY DIFFRACTION99.91
2.44-2.520.25421380.20883374X-RAY DIFFRACTION99.91
2.52-2.610.3041400.21643326X-RAY DIFFRACTION99.86
2.61-2.710.29011510.21353360X-RAY DIFFRACTION99.83
2.71-2.830.26151430.21983329X-RAY DIFFRACTION99.94
2.83-2.980.26071430.20213352X-RAY DIFFRACTION99.89
2.98-3.170.26861420.20523341X-RAY DIFFRACTION99.97
3.17-3.420.27331420.18953353X-RAY DIFFRACTION99.94
3.42-3.760.28541410.17573353X-RAY DIFFRACTION99.77
3.76-4.30.22291480.16043380X-RAY DIFFRACTION99.75
4.3-5.420.16981470.15473363X-RAY DIFFRACTION99.52
5.42-40.450.20961550.18433400X-RAY DIFFRACTION98.59

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