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Basic information

Entry
Database: PDB / ID: 7axy
TitleCrystal structure of a shortened IpgC variant in complex with 3-amino-5-(pyrrolidin-1-yl)-1H-pyrazole-4-carbonitrile
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Dimer / Shigella / Mutant / Magnesium / Chlorine / 3-amino-5-(pyrrolidin-1-yl)-1H-pyrazole-4-carbonitrile
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 / Chem-E9Q / Chaperone protein IpgC
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Crystal structure of a shortened IpgC variant in complex with 3-amino-5-(pyrrolidin-1-yl)-1H-pyrazole-4-carbonitrile
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionNov 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 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)32,9727
Polymers32,6212
Non-polymers3515
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-44 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.517, 57.517, 159.445
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
11ASPASPTYRTYR(chain 'A' and (resid 27 or (resid 28 through 30...AA27 - 4019 - 32
12TYRTYRASNASN(chain 'A' and (resid 27 or (resid 28 through 30...AA42 - 6934 - 61
13ASPASPTYRTYR(chain 'A' and (resid 27 or (resid 28 through 30...AA71 - 7263 - 64
14METMETVALVAL(chain 'A' and (resid 27 or (resid 28 through 30...AA74 - 13066 - 122
15GLNGLNASPASP(chain 'A' and (resid 27 or (resid 28 through 30...AA132 - 148124 - 140
21ASPASPASPASP(chain 'B' and (resid 17 or resid 28 through 40...BB179
22ILEILETYRTYR(chain 'B' and (resid 17 or resid 28 through 40...BB28 - 4020 - 32
23TYRTYRASNASN(chain 'B' and (resid 17 or resid 28 through 40...BB42 - 6934 - 61
24ASPASPTYRTYR(chain 'B' and (resid 17 or resid 28 through 40...BB71 - 7263 - 64
25METMETVALVAL(chain 'B' and (resid 17 or resid 28 through 40...BB74 - 13066 - 122
26GLNGLNASPASP(chain 'B' and (resid 17 or resid 28 through 40...BB132 - 148124 - 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 / Mutation: M1_E9del, D152_E154del
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 , 5 types, 185 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-E9Q / 5-azanyl-3-pyrrolidin-1-yl-1~{H}-pyrazole-4-carbonitrile


Mass: 177.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
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: 1.63→42.24 Å / Num. obs: 38957 / % possible obs: 99.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 24.29 Å2 / CC1/2: 1 / Rsym value: 0.051 / Net I/σ(I): 16.42
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 5.3 % / Num. unique obs: 6172 / CC1/2: 0.85 / Rsym value: 0.7 / % possible all: 99

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Processing

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

6scb


Resolution: 1.63→42.24 Å / SU ML: 0.1951 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.7104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1947 5 %Random selection
Rwork0.1967 37006 --
obs0.1984 38953 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.25 Å2
Refinement stepCycle: LAST / Resolution: 1.63→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 20 180 2255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572154
X-RAY DIFFRACTIONf_angle_d0.76492926
X-RAY DIFFRACTIONf_chiral_restr0.0494320
X-RAY DIFFRACTIONf_plane_restr0.0054388
X-RAY DIFFRACTIONf_dihedral_angle_d14.33871280
LS refinement shellResolution: 1.63→1.67 Å
RfactorNum. reflection% reflection
Rfree0.3822 136 -
Rwork0.2915 2580 -
obs--98.98 %
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)
10.5912667668410.004429881653591.116848900730.314585374699-0.1744165375512.2536273432-0.227314122449-0.0271821273241-0.602864584194-0.131339447816-0.3885711793460.192878368031-0.0752987997677-0.676417267028-0.1251032984460.30585202017-0.05100055592750.09171497632630.624223285448-0.03675573373580.554611216163-39.534745128914.27087391-1.94283899889
20.0445109113348-0.00518817158698-0.01370740086990.002013967134590.003211642674940.005457210874080.009761922514850.155937733601-0.0776718047139-0.172405719553-0.2607719486980.0991079197523-0.197955158056-0.528993925410.0006980448564510.3224796715160.067402162079-0.02153102649920.391756745087-0.06985653439480.291134066973-34.421590504422.8038851323-5.79185282228
30.679756820246-0.05752569383310.3594116473570.00790332092181-0.005564096007670.547432243496-0.4678995813410.03470739486360.228790443687-0.2314801318890.2108007163880.099981623071-0.597003835109-0.0415242068169-0.02359060376570.372143869316-0.0730508832205-0.02749380160590.238007090880.002477782146980.257336653526-20.72471322723.7243301251-7.45571743908
40.136024791849-0.1205927770110.02008976354130.107081946523-0.02587569756490.04596839481840.220873162477-0.112696551090.03700714948420.559029177541-0.2613763937-0.4224678765410.09923995743180.3259930802840.0007450962024860.403424560984-0.0850540769432-0.02240284372140.2355736195840.04975848651450.283193743171-25.61368404582.32149121651-4.13903061581
50.03935622629630.01428159312140.008427798570980.04554112986680.01153362346550.003226988877610.058016951768-0.05983622486260.2617812997030.226218199593-0.214634045044-0.1670492853310.3988408751880.3189021074550.00148181389270.405128368520.0472687023449-0.1428874896290.7212432591880.09402883796460.760783085801-15.131710542-13.5519355427-2.76661871017
60.1265316944840.0960470391634-0.1509870975210.242273368991-0.1108783181690.180902534365-0.04635341320160.357372286956-0.392620176139-0.229890231713-0.0132507177379-0.0711047719410.5452474946920.04923937434229.43934102895E-50.336869719333-0.01775916742940.04267654089740.277325398309-0.01459821979810.232319843233-29.0687581557-20.9532046431-9.58137741732
70.100688454247-0.1141043306070.1939592264670.125161063091-0.2196369682770.367857953312-0.03453137661610.3154277210780.02549284744060.06359155570550.0786592593313-0.100035704701-0.1145892464980.003995961778330.002139195428040.303309645639-0.02451122324590.03949796509940.183371641260.01363874668770.187240775155-28.9904804895-11.2544476981-6.7437865969
80.4925952240780.4739302059080.07164162057510.744524205305-0.3600507511810.592373573314-0.08010369400130.05848166754490.216760848665-0.08980515986710.06312933093960.08312202344880.079786782034-0.1124018067130.0001675977012820.245125759973-0.03391494013870.01094273507690.2328160760880.005664688766940.221707631468-33.5407090322-7.03304923453-16.026108431
90.0179201841629-0.0242268225120.005207632792240.03438152923140.003483509139090.0363708034231-0.214387348175-0.08501565143220.0198543548464-0.1407184263880.444995190829-0.571394433880.02561122078310.328345788568-0.001258615535410.403897315725-0.01871290239270.05225806890810.436042855809-0.01655600612740.422929130972-22.4155714491-5.64392422667-24.7244934822
100.02559720669450.1318988105370.04159455359720.6442784447490.1757676503190.223901078763-0.029940023017-0.0757489537450.0256225329915-0.0420594370402-0.06251789211190.0948451247692-0.0546081281201-0.06420489631197.92902865059E-60.215469145136-0.04617549181780.006067986407760.180532635355-0.02530004280610.188676653621-26.088529769213.8161111966-7.07566263312
110.00284680700975-0.01272514251180.004297640206820.0974796180988-0.02260090934150.006250128123770.175926200813-0.6498733384660.08664621116290.132341355568-0.0869260272971-0.09965111517190.04934716356570.2406349402060.001012352910950.229182824084-0.0868056025186-0.004396069089070.307184067246-0.01620218519820.237628020845-13.088959885111.825979344-9.29178580117
120.0150347898809-0.0134828075356-0.008020074578480.03208071417660.02650101691520.0228926419954-0.168871302317-0.127206379137-0.695090821553-0.2004298455450.034643439232-0.511376881569-0.2998072174550.118507876077-0.001586058404690.336373695027-0.04580139475980.02436596654270.2915996459490.04425778764160.312457813911-13.85490609545.03273328975-11.4142898647
130.3256126754460.375781745422-0.2202389675720.43754932099-0.3044272364370.365109726329-0.04114383083260.0901717913435-0.113212651317-0.1193595984930.02971313459870.03370777217160.0371539258263-0.116365118886-0.00235649525490.238189912968-0.04724843656530.02890565145010.165845572334-0.001345582791610.210826444671-18.92817405565.67112659619-19.4381264107
141.20008818711-0.210016848545-0.3394461085290.101492907671-0.0264670975140.218842704887-0.07796438134050.413293262726-0.0854102874672-0.232543993230.0595320891504-0.02603106367290.252007449321-0.256835167677-0.01723299746020.295068918386-0.1107214308710.03441274335270.219582542311-0.02790378274580.241114451743-18.22338703293.54709296451-29.1188540851
150.1993596124450.0974359610781-0.02416667899870.4951875438410.07820775087530.183458807042-0.01499064688170.6261039189540.183122849371-0.344384621029-0.0419740383236-0.128178954324-0.1361039688220.0254543599511-0.0002115048824080.295242275995-0.08661129992340.01471653398480.3063127435930.03145141792730.278065979109-14.822389315910.8370420607-30.9960413189
160.144290761265-0.01823230303380.1396478405770.0376024215456-0.0869001517340.2646095990680.05535828777950.08341016141990.0414043495186-0.26672051833-0.04798804804930.155338448543-0.165989107652-0.3455143143346.58850616469E-50.3785917701510.0105801050893-0.01887885152240.3220445258860.007800221939210.33731558175-38.2629446856-2.70269230439-25.7885481118
170.08097179661950.0569946212316-0.02204241381790.0810585946903-0.02815412839920.0431515399179-0.1499792606570.3317704413890.532405547802-0.07283771165680.245967270168-0.329949258039-0.551878428306-0.06002808329680.0005202839607940.408821750886-0.0732480257195-0.02229709382440.3699437746850.01119206902490.312298266896-31.7793271927-2.04902781499-33.7846499804
180.06210070636440.0232928463961-0.1308371028560.284744990604-0.08417275925420.2763129308480.204802981450.374543343608-0.00436171261218-0.271740029938-0.298974027485-0.01646594459990.29590836889-0.2786019991570.0009869660947640.38842286265-0.0684002613706-0.0139133678120.438542596707-0.0183330545070.328561346432-36.7573826687-8.19665637264-35.7253270138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 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 21 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 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 'A' and (resid 54 through 78 )
11X-RAY DIFFRACTION11chain 'A' and (resid 79 through 85 )
12X-RAY DIFFRACTION12chain 'A' and (resid 86 through 89 )
13X-RAY DIFFRACTION13chain 'A' and (resid 90 through 121 )
14X-RAY DIFFRACTION14chain 'A' and (resid 122 through 134 )
15X-RAY DIFFRACTION15chain 'A' and (resid 135 through 151 )
16X-RAY DIFFRACTION16chain 'B' and (resid 104 through 124 )
17X-RAY DIFFRACTION17chain 'B' and (resid 125 through 134 )
18X-RAY DIFFRACTION18chain 'B' and (resid 135 through 150 )

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