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- PDB-7o6s: Crystal structure of a shortened IpgC variant in complex with N-(... -

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Basic information

Entry
Database: PDB / ID: 7o6s
TitleCrystal structure of a shortened IpgC variant in complex with N-(2H-1,3-benzodioxol-5-ylmethyl)cyclopentanamine
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Dimer / Shigella / Mutant / Magnesium / Chlorine / N-(2H-1 / 3-benzodioxol-5-ylmethyl)cyclopentanamine
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
N-(1,3-benzodioxol-5-ylmethyl)cyclopentanamine / DI(HYDROXYETHYL)ETHER / Chaperone protein IpgC
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Crystal structure of a shortened IpgC variant in complex with N-(2H-1,3-benzodioxol-5-ylmethyl)cyclopentanamine
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionApr 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 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)33,33911
Polymers32,6212
Non-polymers7189
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-38 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.630, 57.630, 159.184
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
11VALVALTYRTYR(chain 'A' and ((resid 15 through 21 and (name N...AA15 - 407 - 32
12TYRTYRASNASN(chain 'A' and ((resid 15 through 21 and (name N...AA42 - 4834 - 40
13GLYGLYASNASN(chain 'A' and ((resid 15 through 21 and (name N...AA50 - 6942 - 61
14ASPASPTYRTYR(chain 'A' and ((resid 15 through 21 and (name N...AA71 - 7263 - 64
15METMETALAALA(chain 'A' and ((resid 15 through 21 and (name N...AA74 - 7766 - 69
16TYRTYRGLNGLN(chain 'A' and ((resid 15 through 21 and (name N...AA80 - 8172 - 73
17LYSLYSPHEPHE(chain 'A' and ((resid 15 through 21 and (name N...AA83 - 9775 - 89
18ASPASPTYRTYR(chain 'A' and ((resid 15 through 21 and (name N...AA103 - 10495 - 96
19PROPROPROPRO(chain 'A' and ((resid 15 through 21 and (name N...AA106 - 12098 - 112
110ALAALAGLUGLU(chain 'A' and ((resid 15 through 21 and (name N...AA123 - 128115 - 120
111VALVALVALVAL(chain 'A' and ((resid 15 through 21 and (name N...AA130122
112SERSERALAALA(chain 'A' and ((resid 15 through 21 and (name N...AA134 - 149126 - 141
21VALVALTYRTYR(chain 'B' and ((resid 15 through 21 and (name N...BB15 - 407 - 32
22TYRTYRASNASN(chain 'B' and ((resid 15 through 21 and (name N...BB42 - 4834 - 40
23GLYGLYASNASN(chain 'B' and ((resid 15 through 21 and (name N...BB50 - 6942 - 61
24ASPASPTYRTYR(chain 'B' and ((resid 15 through 21 and (name N...BB71 - 7263 - 64
25METMETALAALA(chain 'B' and ((resid 15 through 21 and (name N...BB74 - 7766 - 69
26TYRTYRGLNGLN(chain 'B' and ((resid 15 through 21 and (name N...BB80 - 8172 - 73
27LYSLYSPHEPHE(chain 'B' and ((resid 15 through 21 and (name N...BB83 - 9775 - 89
28ASPASPTYRTYR(chain 'B' and ((resid 15 through 21 and (name N...BB103 - 10495 - 96
29PROPROPROPRO(chain 'B' and ((resid 15 through 21 and (name N...BB106 - 12098 - 112
210ALAALAGLUGLU(chain 'B' and ((resid 15 through 21 and (name N...BB123 - 128115 - 120
211VALVALVALVAL(chain 'B' and ((resid 15 through 21 and (name N...BB130122
212SERSERALAALA(chain 'B' and ((resid 15 through 21 and (name N...BB134 - 149126 - 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 / Mutation: M1_E9del, D152_E155del
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, 196 molecules

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


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


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-45N / N-(1,3-benzodioxol-5-ylmethyl)cyclopentanamine


Mass: 219.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.62 %
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: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 43093 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 21.01 Å2 / Rsym value: 0.059 / Net I/σ(I): 18.8
Reflection shellResolution: 1.58→1.66 Å / Num. unique obs: 6793 / CC1/2: 0.915 / Rsym value: 0.69

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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: 1.58→47.62 Å / SU ML: 0.1633 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.0696
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 2155 5 %random selection
Rwork0.19 40922 --
obs0.1917 43077 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.24 Å2
Refinement stepCycle: LAST / Resolution: 1.58→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 42 187 2402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00942413
X-RAY DIFFRACTIONf_angle_d0.98623292
X-RAY DIFFRACTIONf_chiral_restr0.0548358
X-RAY DIFFRACTIONf_plane_restr0.0073440
X-RAY DIFFRACTIONf_dihedral_angle_d14.05841438
LS refinement shellResolution: 1.58→1.61 Å
RfactorNum. reflection% reflection
Rfree0.3058 139 -
Rwork0.2683 2634 -
obs--98.12 %
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)
19.00517021459-0.4376187396474.087379658875.66501566349-1.226931877715.82000843414-0.04005689021750.123287276001-0.916612856310.12337350787-0.1524540821440.3373952058780.439325705451-1.07800137250.1270441758910.214491314104-0.06780462419490.05387436717420.47063470932-0.07317359538880.423638284603-38.993673106213.7359283285-1.79210019601
29.856041220135.508259031394.868390721153.295413551012.864363919072.53955792581-0.168848358696-0.1928919368820.936196826013-0.221166922807-0.04946319940510.98438849228-0.686600704552-1.121248106080.3007509234740.446824725940.0581366625376-0.0256538529710.417921626454-0.0004640746540050.412044091419-34.673577144223.2635302614-5.52469889131
36.378404082570.2963982995554.966608018662.18147228578-0.2781776254154.77822072475-0.3212325372240.338374513972-0.0332063592986-0.2237090531040.1427381769540.0751462447392-0.3116089220750.2631504401010.1816888939430.329900328519-0.06127684724760.0312479754140.231956324731-0.009382286048720.180805332523-20.560485940424.1331459695-7.78274403928
41.01725078513-1.29346497889-0.4302175342162.477761545141.516314629254.610255194340.04472893910340.0670554507048-0.0571838200134-0.0160423568361-0.07903799276310.0973520083272-0.0304762583467-0.2035328816620.03912477645870.157269601721-0.0421528523110.009862955421140.124678294281-0.007117668262490.121401119386-26.410404022213.6997972556-7.13729551113
57.393167348881.75250317454-2.932589288583.88854200676-0.56378171811.302738972180.310520126119-0.9527465809530.1528875132370.638404095017-0.258064941267-0.260035657099-0.597900079930.429735465139-0.094931160510.196648677204-0.0822566055456-0.003651057653720.273258518184-0.02295223700760.168160494996-13.432641716112.4963035396-9.19967533786
66.18807679686-1.42527699565-4.153426504743.479560515810.7975186525027.116027755640.0069120668569-0.451205363458-0.7654068740690.139894712476-0.16577685387-0.477918964319-0.05211036092670.5543963288390.1708632467090.260617455463-0.0632155323682-0.0123943335060.2572164899720.0357801941680.292947903422-13.83303938885.38660670955-11.5910282453
75.69190888375-0.190008725462-0.3934433510781.68015100137-0.6596065338291.729507426520.098116935008-0.003272787359060.0106222926812-0.117617613673-0.0778738871186-0.0769234413921-0.009084277852260.0261009106943-0.01902069170420.196659360437-0.03345866753250.009585544505160.119247412435-0.01676295106310.148586662072-19.82289233796.19907155892-19.4355569971
88.21617838748-4.180988177685.629075741414.9018706113-3.350198997447.57336945285-0.03453072433130.569253383379-0.514308274443-0.2927871339770.111875601097-0.0720186941730.451390903321-0.0376845893581-0.125682168090.265531516607-0.08503190823440.04429100714060.190557962132-0.02957338635790.198873998733-18.47992884663.50345482206-28.4260290133
98.52585752573-5.315994058891.691271013115.72197314795-1.295176914562.760424181470.05821669645020.6876755486330.0238415617509-0.274835594541-0.161599716815-0.246435498484-0.1023407958990.00559352638750.1173864931770.262085151782-0.08185722839170.02455595760470.2835920810140.03054918074290.249019920481-14.975600481311.1436798014-30.9331115922
104.36445837706-1.13716294260.04338817592040.447333284944-0.2473687834473.040858407840.553365689176-0.08349036750980.1571145644420.467561920733-0.400696375638-0.1631971644870.0517385760745-0.024603688309-0.08364387430380.341955201691-0.04725915246430.01604772288490.2148811496190.03542503978880.241695260995-25.74907469562.33475605986-4.12416956204
112.932610752372.05791241575-1.862764073382.53905598285-0.09243207798743.90064335639-0.08661944241450.389372636062-0.097244959350.0483531459099-0.23806887642-0.9562312857440.05494917782610.30341844099-0.2195943513150.239261664793-0.0789505429713-0.0179586561140.5521632345470.04086060684720.498971404028-15.735947211-8.99214901794-2.59444042889
122.7952935192.790008589192.167696260864.201833671141.196545531875.09571320448-0.008456738207530.309504882422-0.462744674068-0.1824543037930.0557762156328-0.2854658591850.5145427107370.0721525281236-0.07050531499290.3076787417710.007441315039510.03975309384220.185297854697-0.04165607732240.197659138477-28.9825966016-20.7270259041-9.68659197091
137.958371272145.01965547323-0.3629076728617.85359449137-1.05368693397.29900435381-0.04584903347670.1674182806550.0796070816299-0.004453672803980.0434485084110.08892233829850.151323294385-0.05122847587950.0005156888863830.170883937850.006571580303260.03207997629140.118231522072-0.01282623701780.108979398281-29.1026594349-10.7858828524-6.76622154722
143.12662332636-1.110580052813.676263560355.11926563794-1.804128697995.100009170370.0768171930376-0.03646286546520.00839637185499-0.00553850691034-0.02925281349170.2253367128270.181644753316-0.0531879499653-0.03500372571780.164705033635-0.0124681499770.02146277508330.17322450281-0.02166831281510.130829486671-33.6928211315-6.68678943401-16.0782011197
156.733260991244.656830066795.608003129173.850989582954.236154766324.87437685479-0.2175580716540.0377113367862-1.1821708347-0.22310257331.25990512884-1.23855115380.3229104188432.01213517337-0.9941877727370.3438711039650.02862038475870.01882302602910.566074990159-0.01585933630950.4495176962-22.850700148-5.47334996469-24.5578508596
166.7798956789-3.04486692678-5.392586910553.352149839152.193593372578.094977957750.224350196360.02117936115280.277048496028-0.2760563535970.07852055980890.157885596227-0.382162105165-0.336539371294-0.2683605598590.270475307308-0.0236308576747-0.01906080886720.1746749542110.00819619251490.213664438864-38.2983291098-2.67443987919-25.8714040374
176.918026863594.801554696320.02787546510593.65819178407-1.184733672824.48928030070.3565890194390.8104080841890.918319086915-0.04191656094730.1437917337510.247737066164-0.797389622833-0.230810012577-0.3925090724960.3278502124050.02082023212540.05199645182070.2630263868330.06774028830240.247716663812-31.9978584494-1.79694962941-33.8862539213
187.84993258063-5.1388254811-3.471042855588.651958882872.513782027038.724469555670.4155160184670.445532200222-0.571172741231-0.176883875462-0.5133526452960.3645769278280.253688958976-0.8983076417170.1458454930330.268348303084-0.0149325840482-0.01796195494590.36651450713-0.03818603111130.200207188751-36.7085194084-8.5825655902-35.7974331096
192.214493578861.20533611839-0.7129332107428.044160329313.453455921633.87551790790.08661313556110.337025791866-0.821462463307-0.8887452105930.8576516552252.241881592250.814563334448-0.754697171357-0.5949118050690.827981319344-0.0744357233503-0.1738294889950.3362163904320.1392447443971.03116793739-37.94090083134.178493596253.63526750949
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 'A' and (resid 54 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 85 )
6X-RAY DIFFRACTION6chain 'A' and (resid 86 through 89 )
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 121 )
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 134 )
9X-RAY DIFFRACTION9chain 'A' and (resid 135 through 151 )
10X-RAY DIFFRACTION10chain 'B' and (resid 9 through 22 )
11X-RAY DIFFRACTION11chain 'B' and (resid 23 through 33 )
12X-RAY DIFFRACTION12chain 'B' and (resid 34 through 51 )
13X-RAY DIFFRACTION13chain 'B' and (resid 52 through 68 )
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 98 )
15X-RAY DIFFRACTION15chain 'B' and (resid 99 through 103 )
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 )
19X-RAY DIFFRACTION19chain 'A' and (resid 15 through 23 )

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