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- PDB-7o04: Crystal structure of a shortened IpgC variant in complex with [(2... -

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Basic information

Entry
Database: PDB / ID: 7o04
TitleCrystal structure of a shortened IpgC variant in complex with [(2-chloro-5-nitrophenyl)methyl](methyl)amine
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Dimer / Shigella / Mutant / Magnesium / Chlorine / [(2-chloro-5-nitrophenyl)methyl](methyl)amine
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
1-(2-chloro-5-nitrophenyl)-N-methylmethanamine / DI(HYDROXYETHYL)ETHER / Chaperone protein IpgC
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Crystal structure of a shortened IpgC variant in complex with [(2-chloro-5-nitrophenyl)methyl](methyl)amine
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionMar 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 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)33,24912
Polymers32,6212
Non-polymers62810
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-64 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.153, 58.153, 155.167
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
Components on special symmetry positions
IDModelComponents
11A-205-

4AV

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
11SERSERASNASN(chain 'A' and (resid 10 through 20 or (resid 21...AA10 - 202 - 12
12ILEILEGLUGLU(chain 'A' and (resid 10 through 20 or (resid 21...AA31 - 5323 - 45
13ALAALAASNASN(chain 'A' and (resid 10 through 20 or (resid 21...AA55 - 6947 - 61
14ASPASPTYRTYR(chain 'A' and (resid 10 through 20 or (resid 21...AA71 - 7263 - 64
15GLYGLYALAALA(chain 'A' and (resid 10 through 20 or (resid 21...AA75 - 7767 - 69
16TYRTYRLEULEU(chain 'A' and (resid 10 through 20 or (resid 21...AA80 - 9972 - 91
17ASPASPGLNGLN(chain 'A' and (resid 10 through 20 or (resid 21...AA103 - 14495 - 136
18TYRTYRTYRTYR(chain 'A' and (resid 10 through 20 or (resid 21...AA146138
19ASPASPALAALA(chain 'A' and (resid 10 through 20 or (resid 21...AA148 - 149140 - 141
21SERSERASNASN(chain 'B' and (resid 10 or (resid 11 and (name...BB10 - 202 - 12
22ILEILEGLUGLU(chain 'B' and (resid 10 or (resid 11 and (name...BB31 - 5323 - 45
23ALAALAASNASN(chain 'B' and (resid 10 or (resid 11 and (name...BB55 - 6947 - 61
24ASPASPTYRTYR(chain 'B' and (resid 10 or (resid 11 and (name...BB71 - 7263 - 64
25GLYGLYALAALA(chain 'B' and (resid 10 or (resid 11 and (name...BB75 - 7767 - 69
26TYRTYRLEULEU(chain 'B' and (resid 10 or (resid 11 and (name...BB80 - 9972 - 91
27ASPASPGLNGLN(chain 'B' and (resid 10 or (resid 11 and (name...BB103 - 14495 - 136
28TYRTYRTYRTYR(chain 'B' and (resid 10 or (resid 11 and (name...BB146138
29ASPASPALAALA(chain 'B' and (resid 10 or (resid 11 and (name...BB148 - 149140 - 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 , 5 types, 199 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-4AV / 1-(2-chloro-5-nitrophenyl)-N-methylmethanamine


Mass: 200.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9ClN2O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
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: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 35016 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 21.86 Å2 / CC1/2: 0.999 / Rsym value: 0.099 / Net I/σ(I): 15.6
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 5519 / CC1/2: 0.767 / % possible all: 99.5

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Processing

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

6scb


Resolution: 1.74→26.42 Å / SU ML: 0.178 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.8748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2198 1605 5 %
Rwork0.1783 30494 -
obs0.1804 32099 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.96 Å2
Refinement stepCycle: LAST / Resolution: 1.74→26.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 32 189 2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832275
X-RAY DIFFRACTIONf_angle_d0.84443088
X-RAY DIFFRACTIONf_chiral_restr0.055341
X-RAY DIFFRACTIONf_plane_restr0.0069409
X-RAY DIFFRACTIONf_dihedral_angle_d15.49921355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.80.2671440.21272729X-RAY DIFFRACTION100
1.8-1.860.25711430.20192721X-RAY DIFFRACTION100
1.86-1.930.241450.19222740X-RAY DIFFRACTION99.93
1.93-2.020.23281430.18072724X-RAY DIFFRACTION100
2.02-2.130.22091430.17092713X-RAY DIFFRACTION99.96
2.13-2.260.21551450.15992752X-RAY DIFFRACTION100
2.26-2.440.20121460.16582778X-RAY DIFFRACTION99.9
2.44-2.680.21141440.17052743X-RAY DIFFRACTION100
2.68-3.070.23791480.17382812X-RAY DIFFRACTION100
3.07-3.870.22031490.17412820X-RAY DIFFRACTION99.97
3.87-26.420.20521550.18882962X-RAY DIFFRACTION99.78
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)
12.88467895925-4.613047727272.78136484937.50027744602-4.952577430234.746733632090.881660428728-0.777841018261-0.403336138156-0.349852483569-0.1553683109190.3613109556891.05840641586-1.01063241862-0.9274803538120.293937788235-0.08028524397570.09352011742960.2941817442980.1160114938130.316878007531-16.57664603117.66839293392.97896739495
22.82646853564-0.100661572073-0.4967853200874.730239208070.9997821949026.73343262883-0.03738230695040.0551622392510.2447307537860.04878233398410.2561557846-0.0512940251923-0.7921774605690.114722465063-0.2119965041080.231743266444-0.0219953167033-0.008123793649710.1848121590570.0272085125730.165454618593-20.932546976932.93929374940.122765317612
39.13755701018-6.0181141564-5.268785756836.416607976775.151507712944.310727090460.248017217090.310055766272-0.071799920676-0.283156846879-0.216390028855-0.207006131262-0.1338281919940.270492414611-0.03433504027090.232329718219-0.0104933573357-0.005756483009330.2312151254380.02340126114140.160623878219-17.697288963127.2990758691-7.97360445663
45.574184176191.5025404291-0.3813746815937.74033089822-0.7623612094363.10872438025-0.03072393896310.1574173646810.265785631761-0.33797151758-0.02844511632310.49297066437-0.462419865174-0.569617753884-0.02969198459980.2250679164120.0729197668577-0.0306265823560.1815140589770.01133697866040.140160816409-25.772402835228.0010016104-9.65497690399
55.516052469660.7187425816135.307829564487.15918097925.061237733689.65537757531-0.1861712309470.353332631162-0.461612124584-0.1011031109570.39176715541-0.0775319456327-0.408846404401-0.0187941537697-0.2021985569110.265765030759-0.01314480843890.03441232174620.35633255147-0.00729139394250.289458686318-13.13676017137.281521670132.3871327028
65.054820718794.36394326285-2.663395917064.644344921360.1811955151079.44940710030.176575702252-0.149283221894-0.3157714936680.0509370061477-0.174289334433-0.00371238016278-0.425690960885-0.817589306140.08759711067070.2155583166910.0982068743344-0.01726010739680.228705268572-0.02627382606930.230859915175-7.0268519969440.804073216125.130619609
73.01784593579-0.772252084386-2.130985679832.45802847355-1.123004355332.841773417590.114780904831-0.03579152404010.805931580748-0.0234370758336-0.1725690286950.261548472011-0.3908566927310.2354258900950.04853480160620.208365881238-0.012286374374-0.005259758267280.220671254347-0.02233359488090.2766165410053.2451024113641.983745347521.4374218341
88.55712373688-7.03594356322-1.516479152059.033610975411.646224808230.6691747584980.2180252155720.2983309134440.337360183039-0.297503664359-0.0830731028128-0.355914089151-0.1257660189510.0889005057503-0.1204986474830.1525003482210.002070477041020.006406446646230.2765765346930.006799473366810.14196046565111.004552774929.483480858618.2478996853
91.76114861613-0.2978411019711.494771030642.87160933420.495520210644.472521491050.03067768276910.005165569301110.037235187467-0.093085755728-0.03725853572430.047308386429-0.0390843745506-0.06347623027980.01092958301280.0966665411763-0.009423096986760.007205421492250.164202689075-0.006249767134490.115931214334-0.90081513181529.844862487118.9519349533
104.820810539433.368828303060.8824291734796.809253899353.811445578659.17548779744-0.209430222167-0.1820372599230.03203872393840.1831353376690.0010804881989-0.2385712327340.121122857030.02816753962020.2178557579580.1425656674730.0576460347495-0.02366611893220.19763378780.009833025511640.1381128375244.3414387428418.20602159116.8904999723
114.09415524987-3.51138352093-4.581610505613.289097687433.241785685597.42489433235-0.426577380194-0.535845891917-0.164889452888-0.06788184147140.326226425810.1697001010960.6224813103250.4139310569490.03495825393450.176628531971-0.0007398880977960.02813390281670.2529405550130.01450520472490.150795258029-2.1728079342415.330894944115.2195598577
122.72836585128-2.78165520186-1.144164775016.918876606241.33386727073.029849108260.04939906429130.00593617283358-0.0886041362215-0.175888178679-0.03904423361060.152818128539-0.0180716469205-0.010528841635-0.01622414191470.0938097194374-0.02119557266-0.02466437182030.180548058988-0.01068175448540.122711940935-3.7245551682219.48191181876.82898779076
137.16978486735-2.690600709272.378297462844.96620835513-1.930296456342.33534414650.3298344089660.34731890781-0.18477520825-0.387771152212-0.0120748163120.3764331355540.154266799099-0.0946616304489-0.2329524584930.1960220167330.00767175701512-0.01568081694120.226590229679-0.05023681186990.145921087457-6.1763442201717.3598186105-2.21204113135
143.76450747399-1.37620900631-0.7518357109158.86877173775-3.608218300448.24535407087-0.02536663222770.024764472457-0.0511071897384-0.259614859940.1711818674960.2487748406880.1417835631190.0990214768048-0.1261395650540.1357246204070.004626839637270.02565753989790.2360281372540.0007836217109260.1798571000441.6850472222917.6300551965-5.14222908301
159.28343159819-3.156192702685.864209748772.45747956837-2.700270553627.89801974516-0.349696002817-0.356103848114-0.256976152214-0.3603909957750.237625821553-0.1115690438420.681470560346-0.2997077629440.08370757353170.230960105103-0.01855325381170.03870508907250.2954275228350.02471204134330.225715269174-9.9002385329623.705295677321.8086873994
160.913904379578-1.63618399006-2.0458820893.574093614894.427148581545.542982300320.684974374580.389417792986-0.935295142546-0.515553696141-0.50103876997-0.30961433935-0.1447567854881.53112026669-0.3172542651890.4245422168630.09197715548620.1762535968360.441680625630.07303725197450.673722061995-22.06242657985.7695377565219.4137112991
173.21931178453-2.99750912474.079806764492.98062846963-4.346097791487.031794936910.04472864711480.147825426779-0.1850644246350.0951462737775-0.130903913718-0.01504857146860.1206713333650.136455861170.07917855402190.188309368509-0.005606507256720.007878052708370.234356174609-0.01526022092880.1941857459-32.486729193115.464927088615.8566320729
188.61220794616-2.39157668231-4.939988081044.81416294321.89593340597.412390783110.19469393753-0.4216527052180.0246042053884-0.125581793402-0.00659879287815-0.131971263971-0.1125825830460.212658867123-0.1743493621540.13260260727-0.0294074948487-0.001074669273640.135414990612-0.01280267679180.0795849328986-24.642976145920.376225603218.9862268714
193.95327973823-2.56920917356-0.4370862116277.04561259325-0.7237186335962.27612502932-0.05284849150560.08852049489-0.05244081068840.09561928569870.0249277843340.172027899244-0.0554721145387-0.04043197352820.01792930752650.13302365007-0.0162669431056-0.01103387798240.167718312439-0.001291989344470.0814571670768-21.782594194325.90935946719.84476430321
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 99 through 103 )
2X-RAY DIFFRACTION2chain 'B' and (resid 104 through 124 )
3X-RAY DIFFRACTION3chain 'B' and (resid 125 through 134 )
4X-RAY DIFFRACTION4chain 'B' and (resid 135 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 10 through 23 )
6X-RAY DIFFRACTION6chain 'A' and (resid 24 through 32 )
7X-RAY DIFFRACTION7chain 'A' and (resid 33 through 39 )
8X-RAY DIFFRACTION8chain 'A' and (resid 40 through 53 )
9X-RAY DIFFRACTION9chain 'A' and (resid 54 through 78 )
10X-RAY DIFFRACTION10chain 'A' and (resid 79 through 85 )
11X-RAY DIFFRACTION11chain 'A' and (resid 86 through 89 )
12X-RAY DIFFRACTION12chain 'A' and (resid 90 through 121 )
13X-RAY DIFFRACTION13chain 'A' and (resid 122 through 134 )
14X-RAY DIFFRACTION14chain 'A' and (resid 135 through 151 )
15X-RAY DIFFRACTION15chain 'B' and (resid 9 through 21 )
16X-RAY DIFFRACTION16chain 'B' and (resid 31 through 33 )
17X-RAY DIFFRACTION17chain 'B' and (resid 34 through 51 )
18X-RAY DIFFRACTION18chain 'B' and (resid 52 through 68 )
19X-RAY DIFFRACTION19chain 'B' and (resid 69 through 98 )

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