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

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Basic information

Entry
Database: PDB / ID: 7qtd
TitleCrystal Structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase PlaO1 in complex with iron and alpha-ketoglutarate
ComponentsPlaO1
KeywordsBIOSYNTHETIC PROTEIN / Dioxygenase / non-heme iron / Fe(II) / alpha-ketoglutarate / 2-oxoglutarate / terpene synthesis / Phenalinolactone
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / metal ion binding / cytoplasm
Similarity search - Function
: / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
ACETATE ION / 2-OXOGLUTARIC ACID / : / MALONATE ION / PlaO1
Similarity search - Component
Biological speciesStreptomyces sp. Tu6071 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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
C: PlaO1
D: PlaO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,80322
Polymers135,3914
Non-polymers1,41218
Water19,0961060
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17340 Å2
ΔGint-111 kcal/mol
Surface area42370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.124, 108.215, 116.408
Angle α, β, γ (deg.)90.000, 94.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PlaO1


Mass: 33847.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PlaO1 expressed with C-terminal TEV cleavage site 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) / References: UniProt: Q2I752

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Non-polymers , 6 types, 1078 molecules

#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1060 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 34% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→108.21 Å / Num. obs: 160147 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.04 / Rrim(I) all: 0.078 / Net I/σ(I): 13.5 / Num. measured all: 606869 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.843.80.55787796232890.7970.3350.6512.4100
5.52-108.213.70.0271922851880.9990.0170.03236.999.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20-4459refinement
autoPROC1.0.5data reduction
Aimless0.5.17data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GQW
Resolution: 1.75→63.9 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1646 7714 4.82 %
Rwork0.1406 152340 -
obs0.1417 160054 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.27 Å2 / Biso mean: 29.4928 Å2 / Biso min: 9.77 Å2
Refinement stepCycle: final / Resolution: 1.75→63.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9004 0 122 1060 10186
Biso mean--42.58 34.87 -
Num. residues----1121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.24832530.23950975350100
1.77-1.790.2692180.2350595277100
1.79-1.810.22392430.216850625305100
1.81-1.830.22763100.203550495359100
1.83-1.860.23382590.188249945253100
1.86-1.880.24092410.188551365377100
1.88-1.910.20192360.177250775313100
1.91-1.940.20352680.1750785346100
1.94-1.970.20642640.166150335297100
1.97-20.19572140.165351345348100
2-2.030.19962630.162849895252100
2.03-2.070.17432520.141451285380100
2.07-2.110.16772560.136550315287100
2.11-2.150.15362470.124951045351100
2.15-2.20.16622710.122250515322100
2.2-2.250.14562590.125950845343100
2.25-2.310.17122690.129150705339100
2.31-2.370.16882640.130850865350100
2.37-2.440.14862560.126950275283100
2.44-2.520.18162550.12851065361100
2.52-2.610.1872660.136850545320100
2.61-2.710.15932830.14150575340100
2.71-2.840.17312510.139651085359100
2.84-2.990.15572530.133750885341100
2.99-3.170.1632460.13651035349100
3.17-3.420.14632700.127650895359100
3.42-3.760.12852360.12351165352100
3.76-4.310.12122970.108350785375100
4.31-5.420.12132460.11351015347100
5.42-63.90.1962680.17955151541999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.9560.31092.65822.6642.22356.9748-0.20460.3384-0.0707-0.43860.0935-0.1734-0.30970.26980.03660.2209-0.01010.03810.1924-0.01920.16040.1666-11.2162-5.9701
21.629-0.1420.4032.54640.32082.0785-0.00250.16350.0415-0.2714-0.12080.3039-0.122-0.21120.08510.21110.037-0.04350.1893-0.04030.1621-14.9455-14.3332-7.7747
30.9414-0.10690.35060.6122-0.03441.43910.00720.00230.0597-0.011-0.0630.1963-0.091-0.23010.05870.13990.0171-0.01610.1604-0.04390.1957-14.9165-9.06129.6538
40.7611-0.3922-0.17990.63340.23331.62970.03430.0596-0.0524-0.0538-0.11330.08430.1004-0.2030.06360.1435-0.0347-0.0060.1406-0.02010.1626-10.3534-17.032617.3503
51.4488-0.9449-1.24350.80640.79783.92970.01460.06170.00150.0424-0.05590.0161-0.0444-0.07510.00720.1371-0.0207-0.00610.1296-0.00070.1448-5.4043-8.661924.4812
61.10521.18570.2351.41750.62230.7176-0.0380.09720.2936-0.2021-0.06470.2879-0.1618-0.05250.07310.18320.0311-0.04050.1607-0.01190.2152-10.2957-3.77491.7617
70.74660.49790.41720.88620.01482.56340.1479-0.032-0.03340.217-0.01470.42460.1087-0.5307-0.0120.3026-0.0740.08820.24570.00710.3354-15.6759-21.814726.4546
81.7602-0.9230.83265.93-2.42693.5736-0.26790.1593-0.07740.32630.18770.05140.0472-0.41360.02870.1937-0.00220.00640.2812-0.05420.2552-15.23231.217431.1825
92.53760.776-0.5371.8431-0.60642.2199-0.06920.36480.1726-0.57250.032-0.0951-0.0105-0.05860.03540.3130.02570.02070.20450.02590.17248.142514.8556-8.0437
102.4622-0.1707-0.29862.07030.23621.03550.06380.296-0.0048-0.25470.0116-0.49640.06860.405-0.07150.23790.03230.07610.30150.00190.28821.517110.0246-3.5532
112.8544-0.5361-1.69720.09590.32971.3365-0.01660.0393-0.48580.018-0.0668-0.35710.15960.29230.07750.19380.0420.02710.2828-0.01670.392522.73761.8145.4386
120.86240.2338-0.01560.90490.39781.48240.02610.0185-0.0446-0.0294-0.0062-0.1667-0.01260.1612-0.02620.1104-0.0006-0.00290.12690.02160.140810.638313.036815.3568
131.3245-0.7520.98690.7529-0.70115.06460.0234-0.028-0.10780.05890.0012-0.0013-0.02310.0965-0.07350.1262-0.0095-0.0010.12660.00260.13582.97238.751524.6646
142.38170.7411-0.33661.8985-0.55310.61510.00750.1296-0.279-0.2747-0.0756-0.22030.09690.03280.04950.17580.02140.02020.1536-0.01110.15827.2244.06371.1822
151.61760.7449-0.16310.6546-0.29231.11670.01220.0954-0.3469-0.0540.0446-0.42450.12920.1497-0.11640.12020.01860.00050.15430.01030.242714.88228.26068.819
160.6965-0.5503-0.29312.5899-0.41350.8477-0.0931-0.1815-0.06490.6246-0.0144-0.1597-0.01430.25990.03830.2182-0.0193-0.06020.26430.03180.196411.95116.096834.9973
172.0215-0.3237-0.30742.5888-2.47163.5839-0.1621-0.3447-0.230.53930.0610.32480.3167-0.20970.0520.3479-0.01320.07050.25660.01540.1933-3.9455-13.768964.3691
182.08650.094-0.09832.15160.30161.92920.0419-0.3777-0.01450.4126-0.0655-0.3807-0.05870.329-0.00280.2877-0.0319-0.07180.26690.03650.184811.0912-11.893166.8885
190.6856-0.13-0.08460.74010.12761.37190.0107-0.07040.07640.0683-0.0366-0.1664-0.01810.19850.00540.1384-0.0053-0.01570.15280.02520.166610.4245-10.182146.9398
201.82160.7113-1.92010.5572-0.30654.8307-0.0141-0.01920.0441-0.0384-0.0193-0.01080.03790.0952-0.02880.14330.0068-0.00620.12140.00120.13382.2003-8.618534.1089
211.3976-1.2371-0.10741.7208-0.6240.9141-0.0066-0.11250.28120.2183-0.0416-0.3357-0.1610.04870.03430.2034-0.0272-0.03120.16490.00410.18835.3146-2.23655.4719
220.45060.36460.47111.6805-0.08891.2043-0.02810.0550.0558-0.2779-0.0548-0.17930.14880.22280.07880.12740.04480.04660.22630.02260.238812.9889-10.110134.8261
234.2743-0.1493-2.51022.40220.84626.3689-0.1672-0.59270.15630.53570.1025-0.17010.04150.31670.01460.27580.0261-0.0270.2316-0.02380.1335-6.255711.61464.449
243.2551-0.3212-1.24771.58931.08772.69880.067-0.269-0.09730.3764-0.23240.17740.1006-0.0740.05280.2774-0.03420.03720.1977-0.04230.1644-16.081618.695666.2456
252.73490.0274-0.72132.33920.26551.81170.0083-0.1099-0.12230.0736-0.11720.43770.2008-0.36830.09330.2304-0.05260.06060.2465-0.05090.2356-24.711411.609161.1526
261.86230.239-0.89990.0199-0.13971.52510.02160.02-0.26770.018-0.10080.22870.1405-0.24660.03620.1885-0.03920.02590.2219-0.04310.276-24.5147.103849.2479
272.0238-0.7312-1.00290.38580.55430.7887-0.1831-0.4675-0.70520.2290.16370.70660.19270.01860.05930.2509-0.04160.06750.26510.05850.3569-18.1659-0.126459.3718
280.7309-0.2622-0.0541.0299-0.40981.90830.03290.01120.03350.0071-0.03760.1534-0.0503-0.14340.02090.11860.01320.00790.1287-0.02220.1402-11.888515.883438.6036
291.35930.35991.07911.01450.33855.75450.0709-0.0151-0.1166-0.0419-0.02510.04020.0498-0.0319-0.00770.12720.01070.00670.12930.00020.1472-6.17238.968232.9164
301.3257-1.3348-0.23571.29210.11711.071-0.0567-0.0855-0.38190.1895-0.00610.3870.2062-0.10010.01610.1921-0.03950.03920.1672-0.01310.2357-14.96844.266854.557
311.1283-0.568-0.57431.4859-0.15751.56010.1730.16580.0592-0.2631-0.03180.2634-0.1073-0.43360.05230.23270.0499-0.05860.23370.00980.2445-15.958821.620729.1195
321.89331.7763-1.6386.1337-2.6483.3912-0.21390.1127-0.0929-0.190.1526-0.0063-0.1373-0.42580.0030.1996-0.00850.00280.2577-0.04720.2191-14.7808-1.367124.7029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 23 )A9 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 77 )A24 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 169 )A78 - 169
4X-RAY DIFFRACTION4chain 'A' and (resid 170 through 196 )A170 - 196
5X-RAY DIFFRACTION5chain 'A' and (resid 197 through 212 )A197 - 212
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 254 )A213 - 254
7X-RAY DIFFRACTION7chain 'A' and (resid 255 through 274 )A255 - 274
8X-RAY DIFFRACTION8chain 'A' and (resid 275 through 288 )A275 - 288
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 45 )B3 - 45
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 78 )B46 - 78
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 102 )B79 - 102
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 196 )B103 - 196
13X-RAY DIFFRACTION13chain 'B' and (resid 197 through 212 )B197 - 212
14X-RAY DIFFRACTION14chain 'B' and (resid 213 through 231 )B213 - 231
15X-RAY DIFFRACTION15chain 'B' and (resid 232 through 265 )B232 - 265
16X-RAY DIFFRACTION16chain 'B' and (resid 266 through 288 )B266 - 288
17X-RAY DIFFRACTION17chain 'C' and (resid 3 through 19 )C3 - 19
18X-RAY DIFFRACTION18chain 'C' and (resid 20 through 79 )C20 - 79
19X-RAY DIFFRACTION19chain 'C' and (resid 80 through 196 )C80 - 196
20X-RAY DIFFRACTION20chain 'C' and (resid 197 through 212 )C197 - 212
21X-RAY DIFFRACTION21chain 'C' and (resid 213 through 247 )C213 - 247
22X-RAY DIFFRACTION22chain 'C' and (resid 248 through 288 )C248 - 288
23X-RAY DIFFRACTION23chain 'D' and (resid 8 through 23 )D8 - 23
24X-RAY DIFFRACTION24chain 'D' and (resid 24 through 45 )D24 - 45
25X-RAY DIFFRACTION25chain 'D' and (resid 46 through 79 )D46 - 79
26X-RAY DIFFRACTION26chain 'D' and (resid 80 through 112 )D80 - 112
27X-RAY DIFFRACTION27chain 'D' and (resid 113 through 127 )D113 - 127
28X-RAY DIFFRACTION28chain 'D' and (resid 128 through 196 )D128 - 196
29X-RAY DIFFRACTION29chain 'D' and (resid 197 through 212 )D197 - 212
30X-RAY DIFFRACTION30chain 'D' and (resid 213 through 254 )D213 - 254
31X-RAY DIFFRACTION31chain 'D' and (resid 255 through 274 )D255 - 274
32X-RAY DIFFRACTION32chain 'D' and (resid 275 through 288 )D275 - 288

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