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- PDB-7p42: Crystal structure of IpgC in complex with a follow-up compound ba... -

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Basic information

Entry
Database: PDB / ID: 7p42
TitleCrystal structure of IpgC in complex with a follow-up compound based on J2
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Shigella / Follow-up compound
Function / homology
Function and homology information


identical protein binding / cytoplasm
Similarity search - Function
Tetratricopeptide 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
Similarity search - Domain/homology
Chem-5I8 / DI(HYDROXYETHYL)ETHER / Chaperone protein IpgC
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Crystal structure of IpgC in complex with a follow-up compound based on J2
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionJul 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)33,30511
Polymers32,6212
Non-polymers6849
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-47 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.629, 57.629, 159.246
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-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
12ILEILETYRTYR(chain 'A' and (resid 16 through 24 or (resid 25...AA16 - 408 - 32
13TYRTYRTYRTYR(chain 'A' and (resid 16 through 24 or (resid 25...AA4234
14ASPASPASNASN(chain 'A' and (resid 16 through 24 or (resid 25...AA45 - 4837 - 40
15GLYGLYPHEPHE(chain 'A' and (resid 16 through 24 or (resid 25...AA50 - 5942 - 51
16PHEPHEASNASN(chain 'A' and (resid 16 through 24 or (resid 25...AA61 - 6953 - 61
17ASPASPTYRTYR(chain 'A' and (resid 16 through 24 or (resid 25...AA71 - 7263 - 64
18METMETALAALA(chain 'A' and (resid 16 through 24 or (resid 25...AA74 - 7766 - 69
19TYRTYRVALVAL(chain 'A' and (resid 16 through 24 or (resid 25...AA80 - 13072 - 122
110GLNGLNGLNGLN(chain 'A' and (resid 16 through 24 or (resid 25...AA132 - 144124 - 136
111TYRTYRASPASP(chain 'A' and (resid 16 through 24 or (resid 25...AA146 - 148138 - 140
212ILEILETYRTYR(chain 'B' and ((resid 16 through 19 and (name N...BB16 - 408 - 32
213TYRTYRTYRTYR(chain 'B' and ((resid 16 through 19 and (name N...BB4234
214ASPASPASNASN(chain 'B' and ((resid 16 through 19 and (name N...BB45 - 4837 - 40
215GLYGLYPHEPHE(chain 'B' and ((resid 16 through 19 and (name N...BB50 - 5942 - 51
216PHEPHEASNASN(chain 'B' and ((resid 16 through 19 and (name N...BB61 - 6953 - 61
217ASPASPTYRTYR(chain 'B' and ((resid 16 through 19 and (name N...BB71 - 7263 - 64
218METMETALAALA(chain 'B' and ((resid 16 through 19 and (name N...BB74 - 7766 - 69
219TYRTYRVALVAL(chain 'B' and ((resid 16 through 19 and (name N...BB80 - 13072 - 122
220GLNGLNGLNGLN(chain 'B' and ((resid 16 through 19 and (name N...BB132 - 144124 - 136
221TYRTYRASPASP(chain 'B' and ((resid 16 through 19 and (name N...BB146 - 148138 - 140

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chaperone protein IpgC


Mass: 16310.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipgC, ippI, CP0129 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A2U4

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Non-polymers , 6 types, 222 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-5I8 / 2-(4,6-dimethylpyrimidin-2-yl)-3H-isoindol-1-imine / 2-(4,6-Dimethylpyrimidin-2-yl)-2,3-dihydro-1H-isoindol-1-imine / 3466575


Mass: 238.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30 % PEG 4000, 0.1 M TRIS pH 8.0, 0.3 M magnesium chloride
Temp details: 25 Grad

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 50346 / % possible obs: 99.3 % / Redundancy: 10.7 % / Biso Wilson estimate: 19.69 Å2 / CC1/2: 0.999 / Rsym value: 0.055 / Net I/σ(I): 22.39
Reflection shellResolution: 1.5→1.58 Å / Mean I/σ(I) obs: 2.76 / Num. unique obs: 7774 / CC1/2: 0.911 / Rsym value: 0.795

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDS1.2data reduction
XDS1.2data scaling
PHASER7.0.047phasing
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6scb

6scb


Resolution: 1.5→31.12 Å / SU ML: 0.1437 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2186 2498 5 %
Rwork0.1967 47474 -
obs0.1979 49972 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.29 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 41 213 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572390
X-RAY DIFFRACTIONf_angle_d0.77973259
X-RAY DIFFRACTIONf_chiral_restr0.0742352
X-RAY DIFFRACTIONf_plane_restr0.0054444
X-RAY DIFFRACTIONf_dihedral_angle_d19.9239861
LS refinement shellResolution: 1.5→1.53 Å
RfactorNum. reflection% reflection
Rfree0.3048 129 -
Rwork0.2853 2434 -
obs--92.8 %
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)
13.186666342990.6732290087710.09136153348985.443353733441.721442965719.225154748860.0532204604390.152507137839-0.842754701524-0.0238056096529-0.2689086328880.2005665443110.300542970403-0.9464875419080.1522805293620.232700809813-0.04311088628970.02363214445170.393133012204-0.01508908347780.39951236019-39.21213.319-2.142
25.341027202360.8291578703893.215398048795.71852291232-1.967759326523.06899267368-0.05292099679930.0677515347360.0132170603287-0.3344723293110.195634502080.638731550171-0.602908869035-0.780870487733-0.05494493521850.3406672646690.059034274563-0.01445803572370.328770969401-0.01308057338580.267437684119-34.8322.604-6.03
36.142977565921.944876294436.597864901663.403492328270.965542172298.93658811499-0.3258083174610.2742443369940.490834776724-0.3143933127490.06243164240760.105482091489-0.755016574630.1473058875780.2236053943360.259373169879-0.05246916723550.009582612028690.2000816698330.0001132407511930.158848391825-21.20823.364-8.312
42.25233602881-0.24400628489-0.976746375711.548572804730.4973147308583.257007930140.0201185649545-0.00295138685536-0.0180304890950.0162182877007-0.03637364734750.0228591858313-0.002436933449530.02154319015630.01863463459680.171524757461-0.0274383708001-0.0006617733920160.121350746956-0.005550104215790.113410369393-26.05213.64-7.076
56.30269530613-1.04785274475-3.784212959287.725617566541.179433633913.722523002370.100276475058-0.9849487034760.4827772162590.2771506511750.0578109262029-0.299315844974-0.4659015946230.699726441591-0.1044820401150.183015196626-0.0727681694317-0.02917333543210.27793396346-0.03195289634230.170477258913-13.4212.035-9.141
65.64085942662.55781654651-4.587427198334.00749469577-2.639933628467.81172395158-0.180687818936-0.258141077237-0.71204984055-0.05964668488260.041098932572-0.808649542216-0.2814504378610.511038215930.1729465887360.201971962058-0.060339072852-0.0314371685590.203245769828-0.003794128230750.255161132964-13.74.889-11.557
76.497657290260.800420921907-0.4955358093550.843146377506-0.3287931588341.10795686847-0.0377344459244-0.0114863493656-0.174179122171-0.05071782310770.00168823135394-0.040341867805-0.009618299933340.005658432221710.0364155838810.215929931098-0.02833394855250.0119812811510.128076467349-0.007681350420640.164269677397-18.7775.487-19.409
87.87745015131-3.19080934856.924460071984.01420779986-2.557976694858.066020944560.1907590744920.348742862474-0.337548423774-0.388650297631-0.0332490961780.0007674355248320.6187897211140.0875910886718-0.1291997885050.239696374338-0.05343163061250.05070519043090.174126181192-0.02573933151470.179324221108-17.9583.427-28.849
98.40720729534-6.601695922022.970978228577.42714097148-1.864636408292.284169575930.2852776399770.5745380475450.197707325705-0.355116767291-0.285550427556-0.493592482973-0.08717143583860.2232859729540.01242086493590.220552190067-0.08076364512760.04863306314510.2614278999180.01811130559230.206010924719-14.58710.642-30.908
107.303836519625.874891194531.581343563029.795124394054.641781785436.625880159110.47288896433-0.433020022704-0.09718380886140.521212807308-0.414509628257-0.2602763354740.206307250928-0.0180279836644-0.07672328577410.305021255545-0.0303656812470.01080688434020.1859729024980.03986830845980.185205130042-26.2251.826-4.428
113.247719000394.754330980770.8856469139298.152965641443.434201969724.13918680253-0.7331508336230.5028293173941.28290678301-0.171779510762-1.05409748873-0.28539866038-0.551310295557-0.7558728989241.565952380230.391320459176-0.0826029332067-0.1366713033440.7946782064230.0922235160530.658321042652-15.39-13.769-3.099
129.81542751792.495361993311.058646917842.24379311131-0.1125199358924.76186661431-0.129813627460.0968219146763-0.454055368306-0.2820740711380.0672110553211-0.1329377199720.3600209852240.03762624400840.04702106933910.3062609802720.01472150870040.04213538160860.191692817443-0.01162670407520.139675090727-29.796-21.352-9.947
135.339654520693.462942213550.03841314109244.61750554366-0.286036443095.889336019680.0881992798243-0.0173419904990.0215019570020.1348218431360.00948665751047-0.117393416255-0.02248619895910.0563375346588-0.0938731486140.2131116088090.01675354522980.01596004404570.1495161165220.006317600766280.141336108955-29.376-11.188-6.687
145.22087566437-1.417923769091.405557064724.69423910923-1.700619149613.89958891356-0.0305260569775-0.169200889865-0.03268389586930.07868671580670.05623558171550.1537623587720.0916337744529-0.150076096361-0.00692878806750.148200527035-0.02652518678060.002874017122310.139941223684-0.01214862142890.0992261435989-33.225-7.242-16.162
158.938275800225.44382830685.256276985649.111497588275.81208695444.33930609957-0.1565084695520.0617369388977-0.264861069686-0.140632021650.714781689955-1.186252620430.5027857004371.8551860562-0.5179875545960.2797080033860.0229271434813-0.02773786523480.416838388719-0.03009963699560.290857401829-22.257-5.769-24.639
166.78832033655-2.38215680448-3.392037733263.55902816885-0.5091170185579.05708924972-0.00595751260842-0.04643150979790.060063953988-0.1357534358140.1402570257740.328736278848-0.146530117903-0.460069628707-0.1360840536790.191687601023-0.0117167003684-0.04293729691050.133748653368-0.007632240660970.153937412885-38.082-2.558-25.888
175.70395827215-3.11975522903-5.4534265875.895832412244.725351216548.070003706050.04061259580830.3610759555770.571533652012-0.4127766414090.141421172166-0.179023805385-0.5909291266850.0931051406333-0.1288122619680.299244795675-0.0321070617356-0.02822829997340.2513671652380.02051066447010.197696843928-31.324-2.224-34.338
186.46169782658-5.55391372163-5.14619827758.392712209924.547874380186.163542992520.1868088245170.357306593564-0.311170154261-0.221339765395-0.3792471835090.4261344937690.293515910525-0.4709856432110.1873499996320.252599720315-0.0331204221403-0.02896822618730.284304893369-0.01299954044710.207636712524-37.003-8.031-35.655
193.1647154297-2.450317017862.325865361874.49778135688-4.120647002834.16510845396-0.3587638857190.096222235641-0.0103765234805-1.142241475060.2322163894850.8388284447631.174138688260.03563589314770.1047388539130.756553981125-0.131803142364-0.2464308249740.5284294541940.2925869153951.00351128501-38.2263.1373.478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 24:32 )A24 - 32
2X-RAY DIFFRACTION2( CHAIN A AND RESID 33:39 )A33 - 39
3X-RAY DIFFRACTION3( CHAIN A AND RESID 40:53 )A40 - 53
4X-RAY DIFFRACTION4( CHAIN A AND RESID 54:78 )A54 - 78
5X-RAY DIFFRACTION5( CHAIN A AND RESID 79:85 )A79 - 85
6X-RAY DIFFRACTION6( CHAIN A AND RESID 86:89 )A86 - 89
7X-RAY DIFFRACTION7( CHAIN A AND RESID 90:121 )A90 - 121
8X-RAY DIFFRACTION8( CHAIN A AND RESID 122:134 )A122 - 134
9X-RAY DIFFRACTION9( CHAIN A AND RESID 135:151 )A135 - 151
10X-RAY DIFFRACTION10( CHAIN B AND RESID 9:21 )B9 - 21
11X-RAY DIFFRACTION11( CHAIN B AND RESID 28:33 )B28 - 33
12X-RAY DIFFRACTION12( CHAIN B AND RESID 34:51 )B34 - 51
13X-RAY DIFFRACTION13( CHAIN B AND RESID 52:68 )B52 - 68
14X-RAY DIFFRACTION14( CHAIN B AND RESID 69:98 )B69 - 98
15X-RAY DIFFRACTION15( CHAIN B AND RESID 99:103 )B99 - 103
16X-RAY DIFFRACTION16( CHAIN B AND RESID 104:124 )B104 - 124
17X-RAY DIFFRACTION17( CHAIN B AND RESID 125:134 )B125 - 134
18X-RAY DIFFRACTION18( CHAIN B AND RESID 135:150 )B135 - 150
19X-RAY DIFFRACTION19( CHAIN A AND RESID 16:23 )A16 - 23

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