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- PDB-7qtg: Crystal Structure of the Fe(II)/alpha-ketoglutarate dependent dio... -

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Basic information

Entry
Database: PDB / ID: 7qtg
TitleCrystal Structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase PlaO1
ComponentsPlaO1
KeywordsBIOSYNTHETIC PROTEIN / Dioxygenase / non-heme iron / Fe(II) / alpha-ketoglutarate / 2-oxoglutarate / terpene synthesis / Phenalinolactone
Function / homology: / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding / cytoplasm / : / PlaO1
Function and homology information
Biological speciesStreptomyces sp. Tu6071 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.695 Å
AuthorsLukat, P. / Daum, M. / Bechthold, A. / Einsle, O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Thesis / Year: 2011
Title: Structural investigations on the Fe(II)/alpha-ketoglutarate dependent dioxygense PlaO1 from Streptomyces sp. Tu6071
Authors: Lukat, P.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PlaO1
B: PlaO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0006
Polymers67,6962
Non-polymers3044
Water63135
1
A: PlaO1
hetero molecules

B: PlaO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0006
Polymers67,6962
Non-polymers3044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2040 Å2
ΔGint-58 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.923, 108.229, 65.373
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PlaO1


Mass: 33847.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: recombinant PlaO1 expressed with C-terminal TEV-protease cleavage site and Strep-tag II after digestion with TEV protease.
Source: (gene. exp.) Streptomyces sp. Tu6071 (bacteria) / Gene: plaO1, STTU_1451 / Plasmid: pETTSC / Details (production host): modified pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q2I752
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Anaerobically: 60 % Tacsimate pH 7.0, 10 mM Imidazole, 30 mM NaCl, 1.5 mM Fe(II)SO4, 1.5 mM alpha-ketoglutarate, 1.5 mM ascorbate, 2.5 mM PL-CD6 (substrate) Cryo-protechtion: 10 % (2R,3R)-butane-2,3-diol
Temp details: Temperature varied between 298 and 313 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0063 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0063 Å / Relative weight: 1
ReflectionResolution: 2.695→79.74 Å / Num. obs: 23401 / % possible obs: 98.2 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.4
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 14.9 % / Rmerge(I) obs: 1.022 / Num. unique obs: 3412 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5data reduction
Aimless0.7.7data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQW

1gqw


Resolution: 2.695→79.74 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.509 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.5 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.328
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1166 -RANDOM
Rwork0.2397 ---
obs0.242 23225 97.6 %-
Displacement parametersBiso mean: 71.47 Å2
Baniso -1Baniso -2Baniso -3
1--9.7423 Å20 Å20 Å2
2--7.8724 Å20 Å2
3---1.8699 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.695→79.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 12 35 4097
Biso mean--110.65 55.68 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084202HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.945732HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1400SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes724HARMONIC5
X-RAY DIFFRACTIONt_it4202HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion529SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3133SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion18.34
LS refinement shellResolution: 2.695→2.71 Å
RfactorNum. reflection% reflection
Rfree0.3036 23 -
Rwork0.3429 --
obs--97.83 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.8340.40384.75264.80334.04077.5240.31750.2583-0.1640.25830.01751.2567-0.1641.2567-0.3350.7776-0.0864-0.00060.24950.09870.865338.165314.0347.8929
22.6937-1.6194-0.78892.43691.74547.4251-0.08180.95460.34420.95460.13620.95970.34420.9597-0.05441.0727-0.0879-0.12170.44450.03730.722834.71159.702321.374
33.1819-0.76950.84042.1087-0.6612.54190.10870.34780.22450.3478-0.0975-0.0670.2245-0.067-0.01120.8399-0.1017-0.01040.15470.01210.519616.599711.145613.6774
49.90625.40530.15510-4.3362.7180.0539-0.21680.569-0.2168-0.1739-0.41450.569-0.41450.120.6214-0.0003-0.03480.1782-0.02450.61284.5738.28955.036
55.12684.19812.51272.84685.99232.5976-0.21850.68810.17960.68810.12020.67030.17960.67030.09830.7262-0.0064-0.09620.1190.04360.592928.59253.98327.1284
63.63771.10171.54281.0150.25822.1303-0.05840.77330.14750.77330.02530.03270.14750.03270.03320.9938-0.11430.07910.25970.0370.573615.756911.524214.6892
74.8221-2.8234-2.43935.39163.91645.88330.2445-0.072-0.0172-0.0720.04070.6617-0.01720.6617-0.28520.80240.078-0.05970.23010.07110.81337.2859-15.7269-6.5518
88.9247-0.1169-2.45090.09522.623511.48030.1333-1.0884-0.0704-1.0884-0.15290.6388-0.07040.63880.01960.90110.11490.08320.18730.15380.70734.0133-11.6794-20.041
93.5453-0.7616-1.74640.0563-0.64683.39560.2332-0.2868-0.1062-0.2868-0.15230.0712-0.10620.0712-0.08090.90920.09540.01320.16020.03260.580221.1431-9.3545-12.067
105.90972.3163-2.4132.70851.16322.71630.0758-0.3927-0.2993-0.39270.0848-0.283-0.2993-0.283-0.16060.85880.0795-0.01840.2519-0.07550.44489.3941-15.3102-13.2745
1114.90791.89184.88013.4177-2.66876.13190.2890.2643-0.26590.2643-0.3694-0.3083-0.2659-0.30830.08040.60610.04330.02420.1641-0.06010.59663.7565-8.6631-4.2938
126.0197-4.6043-5.41432.39886.84228.00030.1416-0.2904-0.1466-0.29040.08730.6325-0.14660.6325-0.22890.5370.05970.04150.03010.07680.59328.3602-5.3946-5.7744
130-1.3979-1.024105.1729.30010.6193-0.2752-1.4657-0.2752-0.4448-0.1128-1.4657-0.1128-0.17460.90190.17260.16340.20730.11040.654924.9349-2.899-14.0567
1402.13331.38121.5286-1.14160-0.6564-0.61650.1096-0.61650.1525-0.22950.1096-0.22950.50391.06150.0646-0.0520.4157-0.11670.92014.7937-23.3924-12.6305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|10 - A|47 }A10 - 47
2X-RAY DIFFRACTION2{ A|48 - A|82 }A48 - 82
3X-RAY DIFFRACTION3{ A|83 - A|198 }A83 - 198
4X-RAY DIFFRACTION4{ A|199 - A|214 }A199 - 214
5X-RAY DIFFRACTION5{ A|215 - A|233 }A215 - 233
6X-RAY DIFFRACTION6{ A|234 - A|273 }A234 - 273
7X-RAY DIFFRACTION7{ B|11 - B|47 }B11 - 47
8X-RAY DIFFRACTION8{ B|48 - B|81 }B48 - 81
9X-RAY DIFFRACTION9{ B|82 - B|152 }B82 - 152
10X-RAY DIFFRACTION10{ B|153 - B|198 }B153 - 198
11X-RAY DIFFRACTION11{ B|199 - B|214 }B199 - 214
12X-RAY DIFFRACTION12{ B|215 - B|233 }B215 - 233
13X-RAY DIFFRACTION13{ B|234 - B|256 }B234 - 256
14X-RAY DIFFRACTION14{ B|257 - B|272 }B257 - 272

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