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

+
Open data


ID or keywords:

Loading...

-
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 / homologytaurine dioxygenase activity / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / sulfur compound metabolic process / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
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