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

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Basic information

Entry
Database: PDB / ID: 7owv
TitleCrystal structure of IpgC in complex with a follow-up compound based on J20
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Shigella / Mutant
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-2IY / TRIETHYLENE GLYCOL / 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 IpgC in complex with a follow-up compound based on J20
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionJun 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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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)33,1707
Polymers32,6212
Non-polymers5495
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-40 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.788, 57.788, 160.301
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
11ALAALAASNASN(chain 'A' and (resid 14 through 20 or resid 23...AA14 - 206 - 12
12ALAALAPHEPHE(chain 'A' and (resid 14 through 20 or resid 23...AA23 - 5915 - 51
13PHEPHEASPASP(chain 'A' and (resid 14 through 20 or resid 23...AA61 - 6653 - 58
14ASNASNASNASN(chain 'A' and (resid 14 through 20 or resid 23...AA6961
15ASPASPTYRTYR(chain 'A' and (resid 14 through 20 or resid 23...AA71 - 7263 - 64
16METMETALAALA(chain 'A' and (resid 14 through 20 or resid 23...AA74 - 7766 - 69
17TYRTYRTYRTYR(chain 'A' and (resid 14 through 20 or resid 23...AA80 - 10472 - 96
18PROPROILEILE(chain 'A' and (resid 14 through 20 or resid 23...AA106 - 13198 - 123
19SERSERALAALA(chain 'A' and (resid 14 through 20 or resid 23...AA134 - 149126 - 141
210ALAALAASNASN(chain 'B' and ((resid 14 through 18 and (name N...BB14 - 206 - 12
211ALAALAPHEPHE(chain 'B' and ((resid 14 through 18 and (name N...BB23 - 5915 - 51
212PHEPHEASPASP(chain 'B' and ((resid 14 through 18 and (name N...BB61 - 6653 - 58
213ASNASNASNASN(chain 'B' and ((resid 14 through 18 and (name N...BB6961
214ASPASPTYRTYR(chain 'B' and ((resid 14 through 18 and (name N...BB71 - 7263 - 64
215METMETALAALA(chain 'B' and ((resid 14 through 18 and (name N...BB74 - 7766 - 69
216TYRTYRTYRTYR(chain 'B' and ((resid 14 through 18 and (name N...BB80 - 10472 - 96
217PROPROILEILE(chain 'B' and ((resid 14 through 18 and (name N...BB106 - 13198 - 123
218SERSERALAALA(chain 'B' and ((resid 14 through 18 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
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, 157 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-2IY / 3-(4-chlorophenyl)-5-methylsulfanyl-1~{H}-pyrazole-4-carbonitrile


Mass: 249.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8ClN3S
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30 % PEG 4000, 0.1 M TRIS pH 8, 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: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 42465 / % possible obs: 99.5 % / Redundancy: 9.64 % / Biso Wilson estimate: 26.71 Å2 / CC1/2: 0.999 / Rsym value: 0.049 / Net I/σ(I): 21.31
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 9.87 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 6615 / CC1/2: 0.893 / Rsym value: 0.821 / % possible all: 97.5

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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→36.53 Å / SU ML: 0.1787 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2123 5 %random selection
Rwork0.1879 40316 --
obs0.1895 42439 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.7 Å2
Refinement stepCycle: LAST / Resolution: 1.59→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 32 152 2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592375
X-RAY DIFFRACTIONf_angle_d0.76413230
X-RAY DIFFRACTIONf_chiral_restr0.0497347
X-RAY DIFFRACTIONf_plane_restr0.0054437
X-RAY DIFFRACTIONf_dihedral_angle_d14.87281412
LS refinement shellResolution: 1.59→1.63 Å
RfactorNum. reflection% reflection
Rfree0.3237 131 -
Rwork0.2937 2473 -
obs--93.77 %
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)
18.703342714771.12827879011-0.8436248437656.442619390422.294540399145.10412844891-0.1123677386450.0309839899149-1.19757737166-0.362872570357-0.5635427924420.9180698338470.208779278764-1.399306485740.6116294892020.279887303517-0.08218793058290.02159490565850.610109745521-0.170684496540.517641748993-39.452073393513.8455663743-2.14869374479
25.006861005293.187561165843.945843163439.4238543764-0.5783993165254.413797601650.379995068016-0.3877980869320.365404166156-0.139066521194-0.5538256524791.38019220863-0.271748332566-1.474386645710.2018649068810.421831917250.0860245576175-0.01211364904720.472289866703-0.07909063133730.42212358131-34.786290421723.2514956266-5.72624551799
34.073512025252.887153207995.203404809015.58066860051.483124144268.10067622228-0.5198451004970.2727095963320.31981868072-0.3725949262910.1953328787360.0965830165442-0.8336619587220.08621940330180.2977773421630.377896890659-0.09480113655360.02381115872290.224704505626-0.003692342854550.231648984242-20.48427337123.7977894415-7.775378508
43.011159888541.276197886941.022973546414.299754164013.01934134795.134589789040.01640609912290.00197571831088-0.007750970257550.0289233464957-0.1020910622880.0991916555952-0.0215376191813-0.1849676147440.07886004693230.246686239767-0.02113324468060.01494814061360.167248583188-0.004048364820790.194944149464-27.092101134812.9570383053-7.28447971033
57.48920278468-3.52998922425-4.602523803458.370123012140.2348462890577.565713425080.173051426537-1.211527379940.4278070477730.3057340931970.0252841416668-0.475314335237-0.3110958755020.617776845729-0.1671075507130.224470114146-0.109395290776-0.0004212533815110.380131569229-0.05512281952960.315612721057-13.446941625712.3216218528-9.25579807686
67.93609673015-0.09053372975-5.220046784718.56563715718-2.597097684469.285905031590.0765361878665-0.433081474523-0.819796408562-0.6123859716780.000911747846511-1.1939879006-0.05755437859020.588611014784-0.07508211751910.37525874262-0.07205829543240.07943881318440.315379982633-0.004427484802310.43974018469-13.79740733145.192563858-11.833243949
75.69366448231.18260487921-0.7805217174222.32075297166-0.6364531053763.51088152786-0.0809192365560.105880867857-0.141152608203-0.3225928893980.101719616538-0.268736278418-0.1233878459370.0433791851701-0.02627852524250.285550336121-0.05793900761280.06158238746960.157128757448-0.02408717452950.249145009427-18.99719816865.83462088361-19.5489699556
85.37340049443-3.164914363664.683494462572.70851405497-1.89541467557.08350028675-0.1051480193490.697837583477-0.856154476916-0.7386775920020.374183446146-0.2422171565720.06710065849490.00401647778563-0.3339109051620.467493897031-0.1787409285720.1286686379590.313642949596-0.1084507450520.446409842772-18.94929862233.31908400629-28.8095090894
94.62289897183-4.475934686533.306072928747.03786329463-0.8159414735185.71211626454-0.05946678548641.34493695191-0.0992982088749-0.8590902055190.0711078411134-0.521853635678-0.4825933783360.459903611417-0.0003462390599730.553739939213-0.2035020690040.1062303503490.43964088194-0.008484233912820.415544176844-14.952279582410.9001515411-31.1408639517
103.437301255613.32236943622.221253785543.441506020241.187253681368.679615022050.639948370332-0.385752560225-0.06928295030550.616984746265-0.51719301346-0.5324472286750.316901673784-0.056490913908-0.1454707312020.395457843698-0.07661635403230.01085268045150.244520896340.04418957611050.286080961666-26.72360391942.03087315173-4.5609914889
118.05534965234-4.29959844601-1.408377937662.521877425191.275708295566.468074791820.4126030971370.2242617805240.623929076981-0.245897215835-0.838255996578-2.10704124877-0.4502005956210.8025204191880.4161077211690.501292863126-0.09465991660760.02893042267980.8664656524380.1412730494050.739964125043-15.7837983638-9.0010305473-2.38247148426
128.876286208442.48737341202-0.1813770617855.22823997357-0.4392279396856.69728977194-0.2581195127030.199237164758-0.581641714082-0.4481482635220.0242147720817-0.3507343143860.7146039635030.1116102443330.2177447089010.4266388508130.007587700871540.08538198804880.273239609452-0.02705031325250.227841763658-28.9649593194-20.9335179017-9.57783780824
133.506778509794.37062495005-2.44383080017.27429583935-1.669345669749.107860714250.06350721972650.2253429940410.1042506047820.130574283067-0.0305918839601-0.129251638633-0.02879618243780.187024500588-0.06957446444650.2504631440830.02103111055230.02868800541640.1803389451190.008681941349550.196552626486-29.2396644694-10.8764864976-6.70394929687
146.28269164109-0.3558337992741.961063441624.01332797331-2.154861970914.38297162460.0614772917636-0.224006772372-0.0249278499346-0.0226392271184-0.0668076510440.1734648210070.187024946506-0.2162637103180.01414612568490.276482802792-0.01507742436010.01189097676320.210015974155-0.02089160504320.175536204476-33.3676971152-6.79735601544-16.0970865167
153.44144376864.819700059782.462623935659.10900094842.154984326282.46338762141-0.6814926618251.27517033385-1.28043050095-0.8551631821151.58828793629-1.247925030380.225822045193.02082811163-1.090102114640.5183461945090.01096402176950.08779833139110.709055095226-0.01227502680570.425157466984-23.1627227727-6.91348236706-23.6864295964
165.60060435357-2.14263511081-3.578697535664.51220944153-0.1957519240123.356080654270.0266583137784-0.05953921356150.223073097541-0.120041266640.07569125108140.441611097693-0.40540607366-0.391760924371-0.1117477058310.3268358917730.000742437523133-0.06293183393620.290711874723-0.005379208005530.277168983243-38.3436287699-2.74315387693-25.9126583657
173.88515018306-0.929868377891-6.003334900167.953674024861.850326748219.39999065922-0.01163924767460.6523524205051.17623820914-0.3404735272140.329987761287-0.178319347636-1.06732394484-0.302798632605-0.2161951208470.409067908882-0.0191281131886-0.04457848304650.401526896350.03473100657060.32383247486-32.2507627152-1.54553082215-33.7409065733
189.26132726671-5.8653931829-3.825881639823.937533790232.214214676435.6045156610.2272590741910.680686081772-0.249086664269-0.254194969706-0.3298333485960.2856384100060.478007563072-0.507426709110.08621328955790.303308652963-0.0241599939281-0.02428707080030.368078108197-0.03429003185490.301293799277-36.6541203835-8.6531279826-35.9588508245
196.777109473063.862014178140.8947068809216.123685118450.8596556425486.38276538176-0.00557224022798-0.0561108117069-1.58191627481-2.088336750620.03302338676991.131157328241.5112465549-0.7416431299990.06652597204470.750801846414-0.13203553616-0.1521271861430.2654839064980.101444235620.966231736168-38.24359799094.564514213394.11163928087
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 20 )
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 14 through 23 )

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