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- PDB-7b1u: Crystal structure of a shortened IpgC variant in complex with 3-(... -

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Basic information

Entry
Database: PDB / ID: 7b1u
TitleCrystal structure of a shortened IpgC variant in complex with 3-(3,4-difluorophenyl)-1H,4H,6H,7H-imidazo[2,1-c][1,2,4]triazine
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Dimer / Shigella / Mutant / Magnesium / Chlorine / 3-(3 / 4-difluorophenyl)-1H / 4H / 6H / 7H-imidazo[2 / 1-c][1 / 2 / 4]triazine
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-L2K / DI(HYDROXYETHYL)ETHER / Chaperone protein IpgC
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Crystal structure of a shortened IpgC variant in complex with 3-(3,4-difluorophenyl)-1H,4H,6H,7H-imidazo[2,1-c][1,2,4]triazine
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionNov 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: 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)33,39911
Polymers32,6212
Non-polymers7789
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-29 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.418, 57.418, 159.222
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
11THRTHRILEILE(chain 'A' and (resid 24 through 26 or (resid 27...AA24 - 5216 - 44
12GLUGLUASNASN(chain 'A' and (resid 24 through 26 or (resid 27...AA54 - 6946 - 61
13ASPASPTYRTYR(chain 'A' and (resid 24 through 26 or (resid 27...AA71 - 7263 - 64
14METMETVALVAL(chain 'A' and (resid 24 through 26 or (resid 27...AA74 - 13066 - 122
15GLNGLNALAALA(chain 'A' and (resid 24 through 26 or (resid 27...AA132 - 149124 - 141
21THRTHRILEILE(chain 'B' and (resid 24 through 43 or (resid 44...BB24 - 5216 - 44
22GLUGLUASNASN(chain 'B' and (resid 24 through 43 or (resid 44...BB54 - 6946 - 61
23ASPASPTYRTYR(chain 'B' and (resid 24 through 43 or (resid 44...BB71 - 7263 - 64
24METMETVALVAL(chain 'B' and (resid 24 through 43 or (resid 44...BB74 - 13066 - 122
25GLNGLNALAALA(chain 'B' and (resid 24 through 43 or (resid 44...BB132 - 149124 - 141

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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 (E. coli) / References: UniProt: P0A2U4

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Non-polymers , 6 types, 182 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-L2K / 3-[3,4-bis(fluoranyl)phenyl]-1,4,6,7-tetrahydroimidazo[2,1-c][1,2,4]triazine


Mass: 236.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10F2N4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 4000, 0.05 M TRIS (pH 7.0), 0.3 M magnesium chloride

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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: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 41739 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 23.66 Å2 / CC1/2: 1 / Rsym value: 0.073 / Net I/σ(I): 11.4
Reflection shellResolution: 1.59→1.68 Å / Num. unique obs: 6654 / CC1/2: 0.865 / Rsym value: 0.773

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDS1.02data reduction
XDS1.02data scaling
PHASER7.0.047phasing
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SCB

6scb


Resolution: 1.59→47.46 Å / SU ML: 0.1606 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 2086 5 %Random selection
Rwork0.1931 39630 --
obs0.1946 41716 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.21 Å2
Refinement stepCycle: LAST / Resolution: 1.59→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 46 173 2322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532239
X-RAY DIFFRACTIONf_angle_d0.75763037
X-RAY DIFFRACTIONf_chiral_restr0.0482330
X-RAY DIFFRACTIONf_plane_restr0.0055408
X-RAY DIFFRACTIONf_dihedral_angle_d9.63081333
LS refinement shellResolution: 1.59→1.63 Å
RfactorNum. reflection% reflection
Rfree0.3008 137 -
Rwork0.3004 2598 -
obs--98.95 %
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)
10.02486913783-0.0485923206076-0.0251620918110.1738388420450.2083454387730.291704158342-0.04151330422620.1907754262390.9590167065310.0278966699653-0.193911695877-0.519579220088-0.3916175333520.928387926358-0.002057067118730.266977736517-0.109763591742-0.02953194254730.5551546415740.0399914932470.5187134482939.1779641042-13.6083931034-2.06417486768
20.0407621338805-0.00117612206906-0.01334421002890.00381123439467-0.007304262520360.02813413836130.07780995230060.622768931527-0.288613798231-0.278031621159-0.169291449546-0.3780333946310.2702161915150.6717644063073.94192306544E-50.3666933858060.03532624398220.03356840909290.4207983572020.01615573717330.33888794047734.5054295966-22.9354935259-5.73632142883
30.1404792108080.137751215057-0.02170905005080.169840496788-0.1768364092560.166267782413-0.4013153298150.2466527249480.112583985324-0.1341178185390.156430927329-0.1481595193470.440592565208-0.0325349254121-0.003499582380840.359408902528-0.07837569018820.01808846761740.251740873490.001325315256780.24348880192719.9280478758-23.2972844922-6.82452958375
40.00042463971012-0.0205766508505-0.03947492530910.1428724149260.1474241658090.05243225792270.0436254124472-0.2583536786870.1308999189410.390371275863-0.08187804710290.365600450689-0.130845777584-0.5627302992130.001323590272410.432993483411-0.0421565522380.002138189456970.293411738732-0.05154112512340.27486841968924.14884888-1.00999409524-3.40883988047
51.329910404461.007184673181.24254012790.7732239503250.8344647554011.76670774351-0.303750485524-0.09967524486470.194323275924-0.29927041044-0.2617150813720.540974999479-0.241865552065-0.703315922147-0.2362732243460.38325946844-0.1197716310690.1804536663630.665351009014-0.06396434509540.51601502897314.913033511211.4851866071-3.50481713147
60.05831888094840.08711632784280.1512124141440.2992072681980.1734892088370.273357674428-0.0837972626625-0.01940301356610.00130002209334-0.0558922788769-0.01859541235280.0434983621632-0.3461602320060.0947105623642-0.0001387702613980.350511809721-0.0278631588557-0.03464335944950.2781941595040.01988781628560.2326723954728.933849676820.8112909478-9.50805535098
70.02242338485570.0588982393519-0.1629483403770.151641477787-0.00795641637770.5687206309230.005625699875580.21329508251-0.1147930269860.02980054249760.0567881627718-0.1946142001320.03181726196090.06876665680926.94955969241E-50.27198917344-0.0253339905691-0.03344669138460.202888376864-0.01199673913980.19389289472129.149969608611.1602101907-6.75323450657
80.3401513270340.489540267417-0.07303287791140.6268133054440.2212115474430.540100053324-0.03471377550320.0556006174048-0.103622971656-0.07571158879620.064691811708-0.04430148253370.03910610842760.1181320708963.9259855756E-50.232300221172-0.0453122560584-0.004361968639430.275171718048-0.004905533484370.22446699338833.21353040186.94441638902-16.0767025815
90.01701724663820.00147175899924-0.0333799286710.01596777764720.01009527678460.0522651074303-0.00897549494582-0.1185756116180.204804577174-0.1933445149310.8108858923740.488989163951-0.0926828945714-0.5070015198440.001732972345980.3876139024960.0573519772384-0.02493003847210.4843891409710.08872012181950.49705536019822.44295117855.77160543446-24.8420540758
100.1297763202820.0572084924024-0.08204111624190.110546011082-0.009212022799910.254740559013-0.06207445265320.110025100737-0.364369115066-0.1533780391040.0996318925443-0.04913585329810.1065567188220.222896946248-6.52094939065E-50.3783564596010.002111821805910.01910299088810.341904930033-0.01270476873610.32548172096938.23008680192.55278046648-25.6882606269
11-0.0442386222938-0.02925344764970.06885976597590.472064157429-0.3432714986240.193509840212-0.01355568990380.0877732726472-0.101948802761-0.0741161650427-1.24912964615E-5-0.06826147000190.01551838830090.02842848922679.8091998083E-50.247156927145-0.048157502795-0.004861784718540.2080556810830.02152247982740.21644309629926.0083640928-13.9132158474-7.08112977507
120.00462210957332-0.04208122026440.01788354525430.0868344619934-0.0503128983810.01535144778670.21046075734-0.51099207914-0.233301962480.300165635045-0.01835690505140.0321704838659-0.0312177112882-0.1953051805390.000743189915390.226148567162-0.05583926193920.01096853279190.3059702229020.04282461745120.24005979688513.0188846939-11.9076758295-9.34494469066
130.04327942325450.004051040205810.02348610083030.0435443207453-0.02839498718210.02046854741940.0409850693829-0.3950201316330.701328210492-0.227708187071-0.05085267473270.2142114013340.2082176693120.0381114323602-0.0006012697107260.33409619227-0.062262446495-0.02411159694960.262771727613-0.02874518733560.32279251438213.7963037837-5.15637438441-11.4723958134
140.2942131894440.4416262446420.389629993190.358180365420.4214218864620.639542723736-0.02555021805450.1057783491180.0749214911588-0.1330941085610.03363615992870.05173846212360.004002156973620.0788927745506-0.0007356185088090.249311629461-0.0549809314638-0.02476098328910.1824987324910.007033023080930.24746481663618.5934600548-5.71511286777-19.376888232
151.25844830831-0.3422183590560.3436350314630.1657787737760.0193036861770.3399966630950.09791450089950.5687460510480.325558279736-0.4548346435210.06915170088560.0197700467803-0.494845388270.241583396367-0.01858427836390.30751500229-0.091863273815-0.04543799001330.2307538428360.03690428638370.25231797660618.2643847845-3.62866273146-28.8996554983
160.282647621756-0.05161077782860.08975641798320.17019101961-0.08548045026180.1843679420660.1904995354450.377434407713-0.228060618256-0.564500744884-0.1270121702590.0883202366457-0.03726821892070.02460914238510.005057867781830.307305068212-0.0560391896475-0.04297575014270.295738580036-0.02873599466480.30067882799214.9315956865-10.8768378496-30.9879736399
170.05386936040690.0813238569036-0.02585546998630.0845909063543-0.04142402565760.0146131240517-0.02010145808980.28746678447-0.809736149841-0.2358190139710.2472844876240.2144093006890.859224222546-0.184418566892-0.0001654335430510.472879451455-0.0638007070320.033243189570.369186060881-0.04693316027620.33692183934231.7713574721.94313745149-33.7158929412
180.0518930250147-0.009937013949080.105332930250.1439612685410.1138448423340.194720970416-0.05248388706510.1542961058380.242051784137-0.173023230572-0.03398209949360.0350088340699-0.2670563066530.376669628742-0.0002436017549290.398329640636-0.0315766082734-0.0009321130467790.4694792778280.0118132231960.2952627710936.33684742388.63863716333-35.7032229901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 53 )
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 25 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 33 )
6X-RAY DIFFRACTION6chain 'B' and (resid 34 through 51 )
7X-RAY DIFFRACTION7chain 'B' and (resid 52 through 68 )
8X-RAY DIFFRACTION8chain 'B' and (resid 69 through 98 )
9X-RAY DIFFRACTION9chain 'B' and (resid 99 through 103 )
10X-RAY DIFFRACTION10chain 'B' and (resid 104 through 124 )
11X-RAY DIFFRACTION11chain 'A' and (resid 54 through 78 )
12X-RAY DIFFRACTION12chain 'A' and (resid 79 through 85 )
13X-RAY DIFFRACTION13chain 'A' and (resid 86 through 89 )
14X-RAY DIFFRACTION14chain 'A' and (resid 90 through 121 )
15X-RAY DIFFRACTION15chain 'A' and (resid 122 through 134 )
16X-RAY DIFFRACTION16chain 'A' and (resid 135 through 151 )
17X-RAY DIFFRACTION17chain 'B' and (resid 125 through 134 )
18X-RAY DIFFRACTION18chain 'B' and (resid 135 through 150 )

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