[English] 日本語
Yorodumi
- PDB-7qtd: Crystal Structure of the Fe(II)/alpha-ketoglutarate dependent dio... -

+
Open data


ID or keywords:

Loading...

-
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


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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
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

Read more