[English] 日本語
Yorodumi
- PDB-8i98: Crystal structure of TePixD Y8F -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i98
TitleCrystal structure of TePixD Y8F
ComponentsTll0078 protein
KeywordsELECTRON TRANSPORT / Polymer / Photoreceptor / Blue light-using flavin (BLUF) photoreceptor protein / Mutant
Function / homologySensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Acylphosphatase-like domain superfamily / blue light photoreceptor activity / FAD binding / FLAVIN MONONUCLEOTIDE / Tll0078 protein
Function and homology information
Biological speciesThermosynechococcus vestitus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsHu, R. / Lin, L. / Lu, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Key Research and Development Program2020YFA0509700 China
CitationJournal: Progress in Biochemistry and Biophysics / Year: 2023
Title: Structure of the BLUF Protein TePixD Y8F Mutant
Authors: Hu, R. / Zhou, Y. / Lin, L. / Ding, B. / Lu, Q.
History
DepositionFeb 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tll0078 protein
B: Tll0078 protein
C: Tll0078 protein
D: Tll0078 protein
E: Tll0078 protein
F: Tll0078 protein
G: Tll0078 protein
H: Tll0078 protein
I: Tll0078 protein
J: Tll0078 protein
K: Tll0078 protein
L: Tll0078 protein
M: Tll0078 protein
N: Tll0078 protein
O: Tll0078 protein
P: Tll0078 protein
Q: Tll0078 protein
R: Tll0078 protein
S: Tll0078 protein
T: Tll0078 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,43440
Polymers374,30820
Non-polymers9,12720
Water00
1
A: Tll0078 protein
B: Tll0078 protein
C: Tll0078 protein
D: Tll0078 protein
E: Tll0078 protein
F: Tll0078 protein
G: Tll0078 protein
H: Tll0078 protein
I: Tll0078 protein
J: Tll0078 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,71720
Polymers187,15410
Non-polymers4,56310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: Tll0078 protein
L: Tll0078 protein
M: Tll0078 protein
N: Tll0078 protein
O: Tll0078 protein
P: Tll0078 protein
Q: Tll0078 protein
R: Tll0078 protein
S: Tll0078 protein
T: Tll0078 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,71720
Polymers187,15410
Non-polymers4,56310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.273, 162.042, 135.873
Angle α, β, γ (deg.)90.00, 92.60, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1
d_3ens_1
d_4ens_1
d_5ens_1
d_6ens_1
d_7ens_1
d_8ens_1
d_9ens_1
d_10ens_1
d_11ens_1
d_12ens_1
d_13ens_1
d_14ens_1
d_15ens_1
d_16ens_1
d_17ens_1
d_18ens_1
d_19ens_1
d_20ens_1

NCS oper:
IDCodeMatrixVector
1given(-0.99922637355, -0.0388550041265, -0.00607807994005), (-0.0309523183341, 0.872324086126, -0.487947377034), (0.0242612528773, -0.487381757371, -0.872851885597)49.1540291711, 33.6948009771, 126.50053272
2given(-0.657695780095, 0.55710973143, -0.507015786727), (0.582980070562, -0.0498022506901, -0.810958675367), (-0.477043497149, -0.828944197743, -0.292029140422)47.7299598357, 72.7625039118, 117.57267153
3given(-0.056767757961, 0.198421175689, -0.978471490997), (0.203439177274, -0.957190757791, -0.20590860679), (-0.977440495788, -0.210748405067, 0.0139709325248)74.2728932858, 81.0506791926, 87.9793881123
4given(-0.0155765395592, -0.635412219423, -0.772015986119), (-0.629218366228, -0.593828743136, 0.501449570173), (-0.77707246703, 0.493577486555, -0.390563241678)93.0681932923, 45.9302719902, 80.2973786428
5given(-0.590885363199, -0.791384228104, -0.156733822341), (-0.790128021078, 0.528440764977, 0.31056089293), (-0.162948451555, 0.307345670897, -0.937542767407)76.8908875551, 18.6384874471, 105.022130013
6given(0.614426708566, 0.775776045993, 0.143705762809), (-0.590675238721, 0.331551825958, 0.735646755628), (0.523051223268, -0.53688445048, 0.661945998303)-29.011189294, -3.63521625241, 27.0470449512
7given(0.0251159975763, 0.658145799353, 0.752471456907), (-0.175731123211, -0.738081280235, 0.651425050257), (0.984117756674, -0.14859384429, 0.0971190529113)-45.6605277702, 31.7652401199, 34.375454349
8given(0.0330582223865, -0.152891310018, 0.987689931736), (0.679953333478, -0.720843634709, -0.134342542002), (0.732509807597, 0.676024187156, 0.0801291467247)-29.0474392824, 56.4315835987, 9.67068258866
9given(0.617597041187, -0.569982369954, 0.541935413734), (0.774620669126, 0.32154158848, -0.544585921449), (0.136149600366, 0.756129026569, 0.640103258467)-1.04741318634, 39.3417147373, -11.2933152644
10given(0.752096494891, -0.535846424731, 0.383691896547), (-0.479935211873, -0.0463050291939, 0.876081067411), (-0.451678043276, -0.843044751703, -0.291997417537)37.7318438645, 9.75475730599, 184.520881574
11given(-0.725666327469, -0.685852452944, -0.0549071395111), (0.487155601885, -0.455798016146, -0.74493461997), (0.485888671128, -0.567322290474, 0.664874136962)103.909480095, 96.5314988471, 96.3396949298
12given(-0.98837570626, 0.14496554788, -0.0458088769045), (-0.146049946519, -0.989048582263, 0.0212676995785), (-0.0422241210359, 0.0277108616134, 0.998723801534)78.1163957206, 87.0955352205, 66.8959847009
13given(-0.516098634234, 0.587100387558, -0.623662837334), (-0.846289385501, -0.237273930083, 0.476964734641), (0.132047248099, 0.773960087493, 0.619313577468)83.5552803138, 48.7651645835, 56.5649995219
14given(0.0408170511625, 0.0300807813095, -0.99871373022), (-0.649483445159, 0.760367009067, -0.00364225021188), (0.75927941023, 0.648796700144, 0.0505729085894)113.389931762, 34.3634166762, 79.3801534467
15given(-0.0903574674887, -0.757096592843, -0.647024170472), (0.180646862478, 0.626444825861, -0.758243754493), (0.979388706871, -0.185395871739, 0.0801631561037)125.961625681, 63.6755090303, 104.103763986
16given(0.978617087025, 0.198744632149, -0.0530015865332), (0.199829687222, -0.857555151578, 0.473990778503), (0.0487513393421, -0.474446765395, -0.87893320208)29.6030640539, 47.7810739359, 192.840802843
17given(0.479445115864, 0.841005288269, 0.250684036145), (0.865163013491, -0.405103054569, -0.29560865222), (-0.147055571001, 0.358610680659, -0.921831350495)-0.433149605434, 59.4989353266, 168.617347901
18given(-0.0586723531162, 0.525579270307, 0.8487190263), (0.608258879266, 0.692960515513, -0.38707474696), (-0.791567237052, 0.493530297513, -0.360345881984)-10.618641931, 29.3526875671, 146.254825881
19given(0.109669337844, -0.334345562325, 0.936047905446), (-0.212127790748, 0.912159518406, 0.350666242135), (-0.971068708552, -0.237019108796, 0.0291119449098)13.2242742209, -2.25277686821, 155.182974314

-
Components

#1: Protein
Tll0078 protein


Mass: 18715.377 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1) (bacteria)
Gene: tll0078 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DMN3
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 30% (v/v) 2-Methyl-2,4-pentanediol (MPD), 100 mM Sodium acetate/Hydrochloric acid, pH 4.6, 20 mM Calcium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.91973 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91973 Å / Relative weight: 1
ReflectionResolution: 2.54→35.88 Å / Num. obs: 115138 / % possible obs: 98.6 % / Redundancy: 6.2 % / CC1/2: 0.992 / Net I/σ(I): 8.9
Reflection shellResolution: 2.54→2.631 Å / Redundancy: 5.9 % / Num. unique obs: 11342 / CC1/2: 0.788

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→35.88 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 5750 5 %
Rwork0.2031 --
obs0.206 115095 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22385 0 620 0 23005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01323616
X-RAY DIFFRACTIONf_angle_d1.63631848
X-RAY DIFFRACTIONf_dihedral_angle_d20.4363270
X-RAY DIFFRACTIONf_chiral_restr0.0753434
X-RAY DIFFRACTIONf_plane_restr0.0274004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.570.32931800.26163713X-RAY DIFFRACTION99
2.57-2.60.34411730.26683584X-RAY DIFFRACTION98
2.6-2.630.3481680.26553528X-RAY DIFFRACTION96
2.63-2.660.30171970.26613547X-RAY DIFFRACTION95
2.66-2.70.32691970.26143637X-RAY DIFFRACTION99
2.7-2.740.36172130.2783622X-RAY DIFFRACTION99
2.74-2.780.34062140.26693631X-RAY DIFFRACTION99
2.78-2.820.29512310.26143641X-RAY DIFFRACTION100
2.82-2.860.32121820.25583664X-RAY DIFFRACTION99
2.86-2.910.34871960.26593678X-RAY DIFFRACTION99
2.91-2.960.38451980.27863668X-RAY DIFFRACTION99
2.96-3.010.34991910.27313651X-RAY DIFFRACTION99
3.01-3.070.33991880.25313704X-RAY DIFFRACTION99
3.07-3.130.32031960.26373636X-RAY DIFFRACTION99
3.13-3.20.33752100.2553650X-RAY DIFFRACTION99
3.2-3.270.31262150.2533650X-RAY DIFFRACTION99
3.27-3.360.31232000.25543662X-RAY DIFFRACTION99
3.36-3.450.29831840.23363486X-RAY DIFFRACTION94
3.45-3.550.2741800.20913603X-RAY DIFFRACTION97
3.55-3.660.29111910.20323671X-RAY DIFFRACTION100
3.66-3.790.30891780.20213704X-RAY DIFFRACTION99
3.79-3.950.24271920.19443732X-RAY DIFFRACTION100
3.95-4.130.2211820.17193708X-RAY DIFFRACTION100
4.13-4.340.21681800.1673678X-RAY DIFFRACTION99
4.34-4.620.20091730.15373691X-RAY DIFFRACTION99
4.62-4.970.20341840.15923652X-RAY DIFFRACTION98
4.97-5.470.22771800.16123558X-RAY DIFFRACTION95
5.47-6.260.22281950.19273723X-RAY DIFFRACTION100
6.26-7.890.2031820.16873709X-RAY DIFFRACTION99
7.89-35.880.16782000.14643564X-RAY DIFFRACTION94

+
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