[English] 日本語
Yorodumi
- PDB-8ezr: Crystal structure of the HipS(Lp)-HipT(Lp) complex from Legionell... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ezr
TitleCrystal structure of the HipS(Lp)-HipT(Lp) complex from Legionella pneumophila, native protein
Components
  • HipS(Lp)
  • HipT(Lp)
KeywordsTOXIN / toxin-antitoxin complex / legionella pneumophila / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID
Function / homologyHipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / transferase activity / DI(HYDROXYETHYL)ETHER / Toxin HipA / Type II toxin-antitoxin system HipA family toxin
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsStogios, P.J. / Skarina, T. / Michalska, K. / Di Leo, R. / Lin, J. / Ensminger, A. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of the HipS(Lp)-HipT(Lp) complex from Legionella pneumophila, native protein
Authors: Stogios, P.
History
DepositionNov 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HipS(Lp)
B: HipT(Lp)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8394
Polymers47,6972
Non-polymers1422
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.038, 45.038, 393.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-534-

HOH

-
Components

#1: Protein HipS(Lp)


Mass: 11568.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg2369 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A2S6F3Z6
#2: Protein HipT(Lp)


Mass: 36128.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg2370 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic / References: UniProt: A0A2S6F402
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG 1K, 0.1 M Hepes pH 7.5, cryo paratone

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. obs: 29985 / % possible obs: 95.5 % / Redundancy: 14.4 % / Biso Wilson estimate: 42.18 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.024 / Net I/σ(I): 53.2
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 1222 / CC1/2: 0.841 / Rpim(I) all: 0.326 / % possible all: 81.2

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→32.83 Å / SU ML: 0.2276 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8349
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1486 4.99 %RANDOM
Rwork0.2131 28275 --
obs0.2155 29761 95.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.17 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 8 185 3219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00453094
X-RAY DIFFRACTIONf_angle_d0.7114158
X-RAY DIFFRACTIONf_chiral_restr0.0473460
X-RAY DIFFRACTIONf_plane_restr0.0076524
X-RAY DIFFRACTIONf_dihedral_angle_d18.30091175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.32461130.30862139X-RAY DIFFRACTION81.92
2.02-2.090.35081260.28982393X-RAY DIFFRACTION91.83
2.09-2.170.32361280.25982467X-RAY DIFFRACTION93.72
2.17-2.270.32381310.25012527X-RAY DIFFRACTION94.52
2.27-2.390.30721320.25982489X-RAY DIFFRACTION95
2.39-2.540.33121350.25852555X-RAY DIFFRACTION95.93
2.54-2.730.27261330.25262563X-RAY DIFFRACTION96.22
2.73-3.010.28361410.24982668X-RAY DIFFRACTION98.05
3.01-3.440.25391420.22652693X-RAY DIFFRACTION99.51
3.44-4.340.26481450.18252774X-RAY DIFFRACTION99.9
4.34-32.830.221600.18353007X-RAY DIFFRACTION99.62
Refinement TLS params.

Method: refined / 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)
14.60677315539-1.93456422637-2.049423891267.649279658571.505255009695.72168926267-0.614147936479-0.8887907713430.5449616289580.9905699107950.2644983199350.401680024799-0.744723970906-0.8399514059930.2965392655990.9440338015240.440679030841-0.009802314507630.6915306059020.01281974075190.38162384650728.827688569251.9770924517193.45613413
21.47265294791-1.154901563820.8503866833047.555395591591.278270355941.09551434269-0.169192171429-0.479541687816-0.1792426682740.333779989397-0.08905578494590.610557565563-0.86945422149-0.4659125017560.2134944250171.103119576590.37259703859-0.1753993621940.625138645999-0.1572127794930.63422063092631.348031303755.2572747425191.294243629
32.812121382470.1865976545672.643205053086.486350835691.834174960213.24248875914-0.240965263705-0.968032014342-0.03965126269520.469752448827-0.09149585320050.781396883086-0.637982257368-0.9941373460860.3064858049520.9733453602240.557946174166-0.03292050751011.01209322484-0.1396080705680.67891687959421.546253374353.7341692063187.724977434
46.449361235130.711677464459-2.08420999274.89099059268-1.129012527850.8420469367580.611109629745-0.9286030483652.711118435030.01258531065130.217293115357-0.00683061674249-1.751355307530.167462259852-0.7794278547381.488241953420.245818625811-0.08187142284640.628276717722-0.2252386208951.1355599248534.336373660565.4431196937189.965299944
50.62413489583-0.723029728548-0.3796281636423.45115668697-0.625197892120.660421418183-0.137693581233-0.1258779155020.3482878150790.3183395820790.3940011258720.0649029439746-0.372547587412-0.2618376393630.1828695130941.245282094420.68402403561-0.3134017750310.554598786057-0.1503756392810.73464850746927.753964426357.3954087668180.966515467
69.60618241147-4.842064986873.749840297038.6683668422-5.718531927145.451439713810.5476047608190.314008317259-0.0833374600994-2.56842882746-0.2168509643360.841161689339-0.0873812803931-1.33397688515-0.3248698465820.7946525531810.2251024899970.01293038447640.710069673928-0.0107645167120.34909627443931.777706234343.9440405789181.333119835
74.121733663181.94894870426-4.20394611685.95705843196-3.199396333484.59452482153-0.03319513411340.705154514921-0.55078660629-0.477762957046-0.15232020437-0.2438092704120.943872694447-0.6516362439520.2967232291060.551869306861-0.0395729455850.01411557787050.52249205327-0.0007280049341760.47790858608134.729244451630.6942540421186.811802217
84.32223352088-4.435691240514.866777153924.55707098957-4.996661473655.479253025650.7935404623751.29374323804-0.174944277041-0.4753509364170.4484601362820.2951861781130.731183397468-1.12587757807-1.364741854850.6221939421850.0732758146911-0.05972712629630.7798123143220.02587200918830.59861292521326.823205884334.68012457191.111024285
98.74921886885.71665229271-4.596218979195.35779107814-5.710956782878.84558336999-0.249315831476-0.06522361528570.1331945381290.129811516120.272631949105-0.392914390344-0.80713013372-0.635601897016-0.06346615713320.5100493543690.228755147384-0.05275657255030.596265320641-0.07806824616650.42489157998433.998417675243.7028894637188.848116709
105.981476036662.0762363137-5.820568083354.68367131877-1.771289910625.67891830817-0.609389220875-1.07209357748-0.1731504924311.110995847210.152702986283-0.3780661316290.2695756537230.5705338986060.4261931943861.017624384640.384353597755-0.109512799150.614633253759-0.06674073715080.49562735656733.667974381149.7896701061193.596287475
116.067546894580.139625384109-0.02482543434525.00412385832.883880098816.231290781630.3129839036090.8320293617710.61865585772-0.3455817769250.261915437425-1.178177114941.04376968090.522188711542-0.5215088242631.554983078230.03898823506650.1517268627661.231179823510.1841310574941.076659079148.507617810230.5849959333176.376541023
123.64659374640.674292265957-0.2981506468419.143508567044.281067421748.56369852934-0.0841067666814-0.265781042229-0.1214544741780.04568889800830.112057018575-0.4296879645390.310805239522-0.242643890147-0.06315195604210.410631771516-0.04238033320990.03418632280330.3064297312560.02071634990240.3994446477449.056643907733.3328201272182.982977191
131.74050871218-0.7152252679150.5286241158291.319586681940.1363055083224.22014743295-0.1403584569740.1067801149510.00277140649759-0.2182718797120.0163503739426-0.0251694144394-0.305733131250.0767516416150.09750016442250.541589365082-0.10137902122-0.006341476532110.191002155214-0.01075739835560.35487159311744.209804720840.282000619163.388716559
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 8 )AA1 - 81 - 8
22chain 'A' and (resid 9 through 18 )AA9 - 189 - 18
33chain 'A' and (resid 19 through 28 )AA19 - 2819 - 28
44chain 'A' and (resid 29 through 33 )AA29 - 3329 - 33
55chain 'A' and (resid 34 through 54 )AA34 - 5434 - 54
66chain 'A' and (resid 55 through 63 )AA55 - 6355 - 63
77chain 'A' and (resid 64 through 73 )AA64 - 7364 - 73
88chain 'A' and (resid 74 through 80 )AA74 - 8074 - 80
99chain 'A' and (resid 81 through 95 )AA81 - 9581 - 95
1010chain 'A' and (resid 96 through 101 )AA96 - 10196 - 101
1111chain 'B' and (resid 1 through 55 )BC1 - 551 - 15
1212chain 'B' and (resid 56 through 93 )BC56 - 9316 - 53
1313chain 'B' and (resid 94 through 312 )BC94 - 31254 - 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://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