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- PDB-8qh6: Crystal structure of IpgC in complex with a follow-up compound ba... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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

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Experimental details

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Experiment

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

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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

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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

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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

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