[English] 日本語
Yorodumi
- PDB-8qh6: Crystal structure of IpgC in complex with a follow-up compound ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qh6
TitleCrystal structure of IpgC in complex with a follow-up compound based on J20
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / Complex / 3-amino-6-chloro-1H-isoindol-1-one
Function / homologyTetratricopeptide TPR-3 / Tetratricopeptide repeat / Type III secretion system, low calcium response, chaperone LcrH/SycD, subgroup / Type III secretion system, low calcium response, chaperone LcrH/SycD / Tetratricopeptide-like helical domain superfamily / identical protein binding / cytoplasm / 3-azanyl-6-chloranyl-isoindol-1-one / Chaperone protein IpgC
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWallbaum, J.E. / Heine, A. / Reuter, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
LOEWE Center DRUID Germany
CitationJournal: Acs Omega / Year: 2023
Title: Crystallographic Fragment Screening on the Shigella Type III Secretion System Chaperone IpgC.
Authors: Gardonyi, M. / Hasewinkel, C. / Wallbaum, J. / Wollenhaupt, J. / Weiss, M.S. / Klebe, G. / Reuter, K. / Heine, A.
History
DepositionSep 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chaperone protein IpgC
B: Chaperone protein IpgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9217
Polymers32,6212
Non-polymers3005
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-51 kcal/mol
Surface area13790 Å2
Unit cell
Length a, b, c (Å)57.688, 57.688, 159.845
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 24 through 34 or (resid 35...
d_2ens_1(chain "B" and (resid 24 through 27 or (resid 28...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11THRTHRTYRTYRAA24 - 4016 - 32
d_12TYRTYRTYRTYRAA42 - 4434 - 36
d_13PHEPHEGLYGLYAA46 - 5038 - 42
d_14ILEILEGLUGLUAA52 - 5344 - 45
d_15ALAALAASNASNAA55 - 6947 - 61
d_16ASPASPTYRTYRAA71 - 7263 - 64
d_17METMETVALVALAA74 - 13066 - 122
d_18HISHISGLNGLNAA133 - 144125 - 136
d_19TYRTYRILEILEAA146 - 150138 - 142
d_21THRTHRTYRTYRBB24 - 4016 - 32
d_22TYRTYRTYRTYRBB42 - 4434 - 36
d_23PHEPHEGLYGLYBB46 - 5038 - 42
d_24ILEILEGLUGLUBB52 - 5344 - 45
d_25ALAALAASNASNBB55 - 6947 - 61
d_26ASPASPTYRTYRBB71 - 7263 - 64
d_27METMETVALVALBB74 - 13066 - 122
d_28HISHISGLNGLNBB133 - 144125 - 136
d_29TYRTYRILEILEBB146 - 150138 - 142

NCS oper: (Code: givenMatrix: (-0.999959931368, -0.00289158720561, -0.00847197624653), (0.00192616975979, -0.993726378367, 0.111822067626), (-0.00874216953313, 0.111801268604, 0.993692130798)Vector: - ...NCS oper: (Code: given
Matrix: (-0.999959931368, -0.00289158720561, -0.00847197624653), (0.00192616975979, -0.993726378367, 0.111822067626), (-0.00874216953313, 0.111801268604, 0.993692130798)
Vector: -23.8213701136, 46.5469475027, -5.96136445218)

-
Components

#1: Protein Chaperone protein IpgC


Mass: 16310.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: truncated IpgC (IpgC10-151) / Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipgC, ippI, CP0129 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A2U4
#2: Chemical ChemComp-V9U / 3-azanyl-6-chloranyl-isoindol-1-one


Mass: 180.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5ClN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8.0, 32% PEG 4000, 0.3 M MgCl2, seeding

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. obs: 29496 / % possible obs: 99.7 % / Redundancy: 11.9 % / Biso Wilson estimate: 26.07 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.0084 / Rsym value: 0.0081 / Net I/σ(I): 20.3
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 2.91 / Num. unique obs: 4605 / CC1/2: 0.935 / Rrim(I) all: 0.0798 / Rsym value: 0.0763 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36.44 Å / SU ML: 0.1736 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2082 1471 4.99 %
Rwork0.1735 27990 -
obs0.1753 29461 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 16 259 2443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062340
X-RAY DIFFRACTIONf_angle_d0.77233191
X-RAY DIFFRACTIONf_chiral_restr0.0502341
X-RAY DIFFRACTIONf_plane_restr0.006429
X-RAY DIFFRACTIONf_dihedral_angle_d13.0609854
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.54050044573 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.24591280.2162438X-RAY DIFFRACTION97.27
1.86-1.920.30021330.20922517X-RAY DIFFRACTION99.92
1.92-20.23781310.19522493X-RAY DIFFRACTION99.89
2-2.090.23551300.19342480X-RAY DIFFRACTION99.81
2.09-2.20.22111320.16652521X-RAY DIFFRACTION99.92
2.2-2.340.24851320.17242524X-RAY DIFFRACTION99.85
2.34-2.520.22991340.17882545X-RAY DIFFRACTION99.89
2.52-2.770.22231350.18732567X-RAY DIFFRACTION99.93
2.77-3.170.2041340.18252552X-RAY DIFFRACTION99.96
3.17-40.16991380.1562611X-RAY DIFFRACTION100
4-36.440.19461440.1632742X-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)
18.50219559038-3.420572117535.380260306769.19548374399-0.9325430882564.64296299076-0.136637482507-0.4194044465550.270694188846-0.929274927922-0.2970123556451.87550399207-0.739233080019-1.845672523150.3209109264910.4273452164240.146679056801-0.1212334636720.589516696434-0.1000279065790.527539613038-7.5815093732941.156578192724.7376686741
22.0752771025-3.4745510590.6002378821867.57184209918-3.967893263677.90990303327-0.0512035548634-0.5434756897120.5740166839180.187371929825-0.139947739274-0.104905921601-1.22581676611-0.2443299557570.1987013983910.3978820397420.0366379284535-0.05824106705470.338142293281-0.03062323445690.2736662460622.8330158596241.694280540120.7072174048
37.81976441508-6.875989427986.054345613398.0460111934-6.396082094828.564590505150.0648762649370.4673892444850.2964554928550.0406441435217-0.357743275565-0.21018510659-0.2923668012580.7138499010640.2500272601230.178419139581-0.03842300109680.008415646509450.3414373119860.02008032884830.23208095957910.125070855329.818044724418.8071386078
41.663374241391.534285471.707583805721.964220950311.215367452615.97798738037-0.09712506813980.02786226411620.168116517623-0.0564976648493-0.03878634509740.0840838828308-0.178313805651-0.1008894230120.1287468482070.122245593211-0.00217630830477-0.01499496321170.184196305268-0.01018260268520.163158879066-1.4318206726129.933479115719.4769013228
58.98319718699-3.55590114039-1.916740903981.87614659012.484977681796.77758838737-0.227531994182-0.825300604519-0.08961138934710.6210684439980.389617222584-0.4556380719520.5291845233120.996286579433-0.1176452950820.2442103166130.084203007935-0.0421608738120.2927340119610.0004559892940430.2228708492523.9142370455617.456760040117.2336417713
65.94906363358-5.36046414874-7.467173302454.84794307286.745590808269.63645743676-0.340944503784-0.0238422407722-1.193241849220.2154455984360.04900590082050.2245755241580.7788183256880.366960107770.2553303176070.2407401774080.02821428751650.0131143870670.326156763622-0.009738338450150.334481294553-2.3027820174914.614655474315.20605045
71.26674957104-0.240836504213-0.9751364871353.64231865263-0.291826263863.26769877097-0.001479523744060.148494992223-0.0832469583647-0.0875630087916-0.01653484491190.140166032084-0.0674786575874-0.06406350027470.02303910694740.109863577059-0.00544505271535-0.01251089718180.273124865383-0.03263375952540.199654640781-4.1784706004419.20454718977.08405954671
86.26595496765-5.146900523076.084766333094.7052319733-6.179181633348.820872171040.2335910008010.50773104223-0.469229617531-0.372502806384-0.07256352817330.4083089627120.476217670039-0.347698251013-0.1371822427240.1662844697470.01768468594060.005282877476770.370898852888-0.09047244101550.252672303935-6.4475248982817.8223643482-2.83284230132
93.4715696595-2.51340622806-1.101619258792.08053220127-0.007040014135845.686925881830.1198130238510.324053873898-0.23580693957-0.342124688134-0.220257979977-0.1408180034170.1778918124690.4599275790360.09494868384470.2006575372020.05468467223540.01782610280710.400166276612-0.01348253399530.2678033634251.9191643013118.5711982236-4.53107938462
103.84092930088-3.315293819413.443460289136.33120803098-0.08653323464986.24002026698-0.044524076321-1.02275516497-0.2764190677440.08290539395640.192579944795-0.01914422373050.333216410207-0.251678816634-0.1219411902930.167427562236-0.05066585547960.04570636754060.361451900880.01115404066440.208824098399-11.265787014423.907454114522.2775722805
118.941159037310.7722259705855.271826441571.987109367730.6828719045373.134706159660.3593407580070.562353295292-1.30722462713-0.0014359730331-0.262541354595-0.7920899642832.1439087172.02067645113-0.1241314501260.7176290410170.2416673270360.03237767773460.6190172969330.06639815705580.629265439013-18.58457374816.3559610470923.959177682
126.66543121346-5.04717778898-0.8936098677426.160024360810.2113269536719.14150543234-0.07827487646340.148578019622-0.381826263808-0.00920559375244-0.001615493580920.4658944121310.377218483442-0.7751254853140.05544297530270.213849408288-0.09767634702420.009489936425770.324506857571-0.03893858793640.203263582124-32.850879917214.802596064617.4051059694
132.75410544422-2.869775399291.465147648364.09945260578-1.259226995115.06176883036-0.00093155505872-0.271885037253-0.3216974805560.00986151869830.06406781935930.107922749336-0.0275175573408-0.042481495994-0.0519009794540.179540648557-0.05105385203710.03106448608240.210023038415-0.02939350854520.152270426267-24.802152031419.911802416220.081646141
142.60890429261-0.2570825945770.5709399498538.53509604042-3.102864425454.02689665346-0.0614940818212-0.08846197233330.08720478887090.260776645743-0.01694240319280.192432144603-0.0393079532355-0.2681523695090.07730290927680.116633995599-0.00759563730583-0.001875050171660.222439846261-0.02199246497050.133587233982-22.587736767125.558669387810.6255858743
152.40867885906-1.576002475022.403580109923.54011974949-3.584465976744.125235153220.705615805420.676607837497-1.1473449878-0.110713671898-0.260148362237-0.2712680293811.501382774731.09733380215-0.3879152903460.4028094388270.04773530972140.03217996678450.327120684294-0.008640249302720.383427574487-15.710245754716.88509730712.2787340115
164.69243989713-2.37285528756-1.752989933168.553347103892.017923698445.87032532210.007470497325450.2555333094110.426612689742-0.292785949810.0558630683642-0.024349300279-0.750172507785-0.0418734013583-0.04817468083410.20236127037-0.00975309538353-0.0266358123950.2568882986820.04317774351830.186141204875-21.37291589932.40322040860.816422093116
176.63269442753-4.22595218568-3.629910910349.515051226456.159462085159.17395378660.3259808694110.5803960763460.283995947108-0.592852051201-0.038425563395-0.786293764489-0.6293407928420.536950156795-0.2526102630440.213998507130.005010743479070.01325764479540.3687331219740.0516408571670.245229266676-17.337046818526.7216040547-7.90092327705
185.94940802867-0.116331289239-0.6622624521386.242678423094.087844617387.72888747881-0.09680464118630.01953878237950.163326401851-0.672224750314-0.1301122662230.72063704799-0.594040281958-0.9275857398870.2045837242820.2448598061680.0605202442765-0.06089063752040.38284100426-0.001410326428140.219924356806-25.934379484627.9577746093-9.05104538483
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 32 )AA24 - 321 - 9
22chain 'A' and (resid 33 through 39 )AA33 - 3910 - 16
33chain 'A' and (resid 40 through 53 )AA40 - 5317 - 30
44chain 'A' and (resid 54 through 78 )AA54 - 7831 - 55
55chain 'A' and (resid 79 through 85 )AA79 - 8556 - 62
66chain 'A' and (resid 86 through 89 )AA86 - 8963 - 66
77chain 'A' and (resid 90 through 121 )AA90 - 12167 - 98
88chain 'A' and (resid 122 through 134 )AA122 - 13499 - 111
99chain 'A' and (resid 135 through 151 )AA135 - 151112 - 128
1010chain 'B' and (resid 9 through 21 )BB9 - 211 - 13
1111chain 'B' and (resid 28 through 33 )BB28 - 3320 - 25
1212chain 'B' and (resid 34 through 51 )BB34 - 5126 - 43
1313chain 'B' and (resid 52 through 68 )BB52 - 6844 - 60
1414chain 'B' and (resid 69 through 98 )BB69 - 9861 - 90
1515chain 'B' and (resid 99 through 103 )BB99 - 10391 - 95
1616chain 'B' and (resid 104 through 124 )BB104 - 12496 - 116
1717chain 'B' and (resid 125 through 134 )BB125 - 134117 - 126
1818chain 'B' and (resid 135 through 150 )BB135 - 150127 - 142

+
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