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

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Basic information

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


taurine dioxygenase activity / sulfur compound metabolic process / 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 / MALONATE ION / SUCCINIC ACID / PlaO1
Similarity search - Component
Biological speciesStreptomyces sp. Tu6071 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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)136,21915
Polymers135,3914
Non-polymers82711
Water19,2221067
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16000 Å2
ΔGint-71 kcal/mol
Surface area41950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.894, 108.172, 115.033
Angle α, β, γ (deg.)90.000, 93.870, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 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

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Non-polymers , 5 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-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1067 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 36 % Tacsimate pH 7.0 soak: 15 min 375 mM Na succinate, 250 mM NaHCO3 Cryo: 100 % Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→78.72 Å / Num. obs: 226503 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.024 / Rrim(I) all: 0.046 / Net I/σ(I): 19.4 / Num. measured all: 857403 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.630.548123600330390.8440.3290.6412.499.9
4.89-78.720.01427291729010.0080.01661.199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20-4459refinement
autoPROC1.0.5data reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gqw
Resolution: 1.55→48.46 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1729 11058 4.88 %
Rwork0.1505 215340 -
obs0.1516 226398 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.29 Å2 / Biso mean: 27.7524 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 1.55→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8943 0 77 1067 10087
Biso mean--35.89 33.59 -
Num. residues----1117
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 (%)
1.55-1.560.24893740.244971617535100
1.56-1.580.25523980.237270787476100
1.58-1.60.24833530.224672087561100
1.6-1.620.24563640.216371597523100
1.62-1.640.22784010.203171917592100
1.64-1.670.21513930.189270947487100
1.67-1.690.19873600.177171827542100
1.69-1.720.2093830.174171277510100
1.72-1.740.19253720.171671437515100
1.74-1.770.21523460.166672617607100
1.77-1.80.19543610.170371237484100
1.8-1.830.19583980.163371657563100
1.83-1.870.18673390.165271727511100
1.87-1.910.20183470.162672037550100
1.91-1.950.15753720.142871797551100
1.95-1.990.17413410.141472327573100
1.99-2.040.17243470.140571357482100
2.04-2.10.17583730.137171767549100
2.1-2.160.1433700.132671547524100
2.16-2.230.14823590.129971707529100
2.23-2.310.16463750.136172027577100
2.31-2.40.1583790.137571557534100
2.4-2.510.16573590.138572237582100
2.51-2.640.17913860.147671507536100
2.64-2.810.17273720.152471657537100
2.81-3.030.18653610.159772097570100
3.03-3.330.17043650.147971847549100
3.33-3.810.14913520.133572327584100
3.81-4.80.1343910.118472337624100
4.8-48.460.19313670.17567274764199
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)
12.95780.21771.3542.40090.12566.1908-0.10550.3777-0.0241-0.361-0.0754-0.156-0.06120.18410.23350.23470.00890.01510.2081-0.0040.1658-0.1687-11.1663-6.4042
22.3352-0.06061.0711.52030.772.18070.04870.22060.086-0.3636-0.16730.0966-0.01730.0370.08950.24660.0343-0.02180.1769-0.01750.165-9.9477-18.2854-10.1482
31.9083-0.32050.89962.21340.27161.69140.00120.03320.0928-0.2068-0.1760.5126-0.096-0.31150.12740.2080.031-0.05410.2264-0.06420.2479-19.0045-11.6338-6.203
41.1719-0.48020.67250.2066-0.14911.31510.0653-0.03370.254-0.0287-0.21720.348-0.1203-0.28690.05870.17130.0446-0.03920.2031-0.06170.3082-21.1748-6.59334.7071
50.75660.2013-0.010.71460.32720.8318-0.02540.03590.04140.0063-0.03130.0903-0.01740.00810.05480.1292-0.00370.00010.1276-0.01680.1304-5.1635-11.37379.6875
64.5718-3.85931.50366.6943-2.20542.3031-0.166-0.08850.05410.17370.14180.788-0.2391-0.65870.01130.15810.0237-0.00010.297-0.04350.2645-21.0564-12.318820.4051
70.6514-0.0931-0.12070.83670.21881.4492-0.01320.0121-0.0095-0.0077-0.07560.10550.0321-0.08340.0840.1406-0.0157-0.00470.1465-0.00430.1389-7.9938-13.564419.9868
80.97090.94010.1091.29490.50120.907-0.04330.07350.2632-0.2024-0.05640.2946-0.1015-0.0980.07160.16310.0204-0.040.1404-0.0050.1897-10.0467-3.60011.3937
90.85070.27160.15841.1995-0.09232.21990.1030.00650.04220.1206-0.01150.39480.1788-0.4250.00130.2877-0.08050.08140.2551-0.00910.2783-15.3508-22.058826.2959
101.5480.376-0.16163.4956-1.61493.455-0.261-0.0407-0.12330.15240.19530.15010.1831-0.40090.01330.29010.00340.01960.3096-0.04450.3358-14.01680.963530.8647
112.19480.6167-0.51451.7393-0.36031.5544-0.07090.25180.0651-0.5390.0463-0.11230.05050.0374-0.00040.25920.00890.01920.16810.01510.12787.660414.7772-8.2194
122.2884-0.1207-0.45132.10560.07551.14320.0150.0899-0.0023-0.2320.0182-0.51970.0310.2791-0.04260.21590.0230.06220.24040.01180.275721.58079.8199-4.4163
131.7341-0.3289-0.87550.09370.27730.86580.0438-0.03-0.41030.0963-0.0917-0.3950.20220.28220.09820.19160.05480.0250.2470.00240.384921.72241.41065.4358
140.57290.1825-0.10250.72070.34971.23080.0017-0.0103-0.0334-0.02380.006-0.12320.00340.1371-0.01480.1205-0.00220.00280.14640.01650.147910.858913.116514.9718
151.2826-0.54890.93790.9311-0.33584.87730.0339-0.0452-0.06090.0387-0.0602-0.04240.16540.06260.0060.1136-0.01180.0040.122800.12083.3928.599624.3976
161.06341.03520.00421.5466-0.03280.99630.00660.0683-0.2847-0.148-0.0045-0.35630.14660.1155-0.00540.16320.02780.01520.1509-0.00170.204111.79092.38842.9356
171.30590.3341-0.34231.54620.21081.98080.1231-0.1497-0.04510.19570.0244-0.2582-0.14970.284-0.12210.2295-0.0474-0.04480.2021-0.00570.216413.071621.728327.4701
181.3531-0.15990.04283.19151.27492.4232-0.1298-0.0845-0.05450.15360.1325-0.026-0.15010.32340.01280.3094-0.01120.01950.33970.06170.314911.7446-1.371332.5038
191.7514-0.2720.51261.4094-0.36421.566-0.0817-0.2845-0.060.55530.0144-0.0921-0.1578-0.0050.03820.2784-0.011-0.00670.18090.02330.13233.0536-14.737766.8357
202.12580.12590.5562.37250.14011.56180.0209-0.14380.09240.2355-0.0664-0.5632-0.10590.30580.05020.2185-0.047-0.07260.23110.05210.241316.8065-9.898864.4457
210.601-0.18360.09910.7518-0.10421.2694-0.0151-0.04340.1090.0813-0.057-0.2309-0.07650.17110.04860.1406-0.013-0.01690.16030.03210.185310.2824-8.12850.5247
222.58551.77730.13023.67430.4941.489-0.07080.02850.1341-0.11210.004-0.6148-0.15940.6241-0.00980.143-0.035-0.00040.3030.04930.26719.5355-11.276637.4706
230.8887-0.0112-0.4451.2922-0.23112.3414-0.0102-0.0278-0.03840.0113-0.086-0.02940.06090.15210.09330.12890.0227-0.00370.15010.01740.13577.7958-16.476540.9807
241.29050.0031-1.23061.25680.0064.34470.04440.04140.0337-0.0799-0.0723-0.079-0.1440.09720.02010.14660.0101-0.0110.14050.00360.13372.5131-8.411233.8174
251.1731-1.0363-0.0411.601-0.58531.105-0.0258-0.06710.23490.2045-0.0496-0.3443-0.1370.14660.0560.179-0.0276-0.02930.15550.01320.18938.1713-2.632555.8687
260.9211-0.40640.25970.8301-0.09552.83660.1310.06480.0491-0.1781-0.0337-0.32560.17680.3685-0.00690.31080.07420.07860.22970.01240.257512.89-21.698732.0435
271.68530.47550.47545.6362.79344.0479-0.27140.0973-0.0589-0.29910.2761-0.16250.11450.5689-0.00150.3174-0.0031-0.00350.3330.05870.311812.41190.990326.1833
284.0417-0.4149-3.16422.46741.24087.8035-0.2226-0.4844-0.04870.4639-0.0116-0.12520.19230.14260.2550.24840.0046-0.02080.21760.00440.1493-4.946111.011463.5877
293.27390.389-1.50361.27250.68172.29240.0782-0.3269-0.0610.4656-0.20450.1580.1570.07510.08990.2944-0.03680.04330.1864-0.02510.1586-14.87218.38966.0752
302.5166-0.0748-0.72012.2809-0.20851.7320.0698-0.1331-0.06710.1807-0.03810.44030.0125-0.2446-0.04140.2387-0.02830.0580.2151-0.02340.23-23.533511.448961.2087
311.4840.4109-0.79990.1077-0.22131.52270.0130.0438-0.28830.027-0.08770.28660.1783-0.25310.04520.2003-0.04210.03320.2262-0.0230.3108-24.03675.966149.725
320.9168-0.0833-0.21661.1034-0.34921.2092-0.0115-0.0613-0.06850.0728-0.01410.08070.01870.00220.0250.1251-0.0010.00340.1203-0.01390.1145-7.682111.334246.9275
333.94682.8628-1.28924.7998-1.69332.0304-0.14110.2202-0.0714-0.20290.16550.61510.2479-0.4749-0.06730.1496-0.02660.00060.2576-0.02740.2415-22.055412.122934.4882
340.87160.05580.12671.182-0.1531.460.0113-0.00350.01520.0811-0.02180.09090.0292-0.0740.00840.11170.01920.01110.1304-0.00690.1256-11.614816.61638.7429
351.34630.41750.84050.86270.41423.68390.002-0.0393-0.0416-0.0293-0.09290.10010.155-0.13550.07580.14490.00750.00930.15010.00780.1471-5.4938.450433.0554
361.1743-1.1952-0.01741.32520.12471.0373-0.0239-0.1007-0.31660.1678-0.00950.31070.1546-0.07890.01210.1909-0.02680.03550.14920.00650.1973-13.81033.372954.7159
371.2416-0.3745-0.13141.9907-0.2752.35310.12710.0377-0.0252-0.1615-0.06510.2884-0.2189-0.4333-0.03480.20990.0465-0.04790.2434-0.00080.2585-15.581722.010429.3011
381.4876-0.01760.04492.9689-1.21512.7544-0.140.05450.0298-0.20640.07570.0261-0.1233-0.32090.0490.28410.00820.01370.2958-0.04510.3189-13.9903-1.532525.0542
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 45 )A24 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 78 )A46 - 78
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 112 )A79 - 112
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 150 )A113 - 150
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 169 )A151 - 169
7X-RAY DIFFRACTION7chain 'A' and (resid 170 through 212 )A170 - 212
8X-RAY DIFFRACTION8chain 'A' and (resid 213 through 254 )A213 - 254
9X-RAY DIFFRACTION9chain 'A' and (resid 255 through 274 )A255 - 274
10X-RAY DIFFRACTION10chain 'A' and (resid 275 through 288 )A275 - 288
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 45 )B3 - 45
12X-RAY DIFFRACTION12chain 'B' and (resid 46 through 80 )B46 - 80
13X-RAY DIFFRACTION13chain 'B' and (resid 81 through 102 )B81 - 102
14X-RAY DIFFRACTION14chain 'B' and (resid 103 through 196 )B103 - 196
15X-RAY DIFFRACTION15chain 'B' and (resid 197 through 212 )B197 - 212
16X-RAY DIFFRACTION16chain 'B' and (resid 213 through 254 )B213 - 254
17X-RAY DIFFRACTION17chain 'B' and (resid 255 through 274 )B255 - 274
18X-RAY DIFFRACTION18chain 'B' and (resid 275 through 288 )B275 - 288
19X-RAY DIFFRACTION19chain 'C' and (resid 4 through 45 )C4 - 45
20X-RAY DIFFRACTION20chain 'C' and (resid 46 through 79 )C46 - 79
21X-RAY DIFFRACTION21chain 'C' and (resid 80 through 150 )C80 - 150
22X-RAY DIFFRACTION22chain 'C' and (resid 151 through 169 )C151 - 169
23X-RAY DIFFRACTION23chain 'C' and (resid 170 through 196 )C170 - 196
24X-RAY DIFFRACTION24chain 'C' and (resid 197 through 212 )C197 - 212
25X-RAY DIFFRACTION25chain 'C' and (resid 213 through 254 )C213 - 254
26X-RAY DIFFRACTION26chain 'C' and (resid 255 through 274 )C255 - 274
27X-RAY DIFFRACTION27chain 'C' and (resid 275 through 288 )C275 - 288
28X-RAY DIFFRACTION28chain 'D' and (resid 9 through 23 )D9 - 23
29X-RAY DIFFRACTION29chain 'D' and (resid 24 through 45 )D24 - 45
30X-RAY DIFFRACTION30chain 'D' and (resid 46 through 78 )D46 - 78
31X-RAY DIFFRACTION31chain 'D' and (resid 79 through 112 )D79 - 112
32X-RAY DIFFRACTION32chain 'D' and (resid 113 through 150 )D113 - 150
33X-RAY DIFFRACTION33chain 'D' and (resid 151 through 169 )D151 - 169
34X-RAY DIFFRACTION34chain 'D' and (resid 170 through 196 )D170 - 196
35X-RAY DIFFRACTION35chain 'D' and (resid 197 through 212 )D197 - 212
36X-RAY DIFFRACTION36chain 'D' and (resid 213 through 254 )D213 - 254
37X-RAY DIFFRACTION37chain 'D' and (resid 255 through 274 )D255 - 274
38X-RAY DIFFRACTION38chain 'D' and (resid 275 through 288 )D275 - 288

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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