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- PDB-7azv: Crystal structure of a shortened IpgC variant in complex with 4-(... -

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Basic information

Entry
Database: PDB / ID: 7azv
TitleCrystal structure of a shortened IpgC variant in complex with 4-(trifluoromethyl)benzene-1-carboximidamide
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Dimer / Shigella / Mutant / Magnesium / Chlorine / 4-(trifluoromethyl)benzene-1-carboximidamide
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 / 4-(trifluoromethyl)benzenecarboximidamide / Chaperone protein IpgC
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Crystal structure of a shortened IpgC variant in complex with 4-(trifluoromethyl)benzene-1-carboximidamide
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionNov 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 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)33,1639
Polymers32,6212
Non-polymers5427
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.368, 58.368, 155.040
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-

FBF

21A-205-

FBF

31A-205-

FBF

41A-205-

FBF

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
11GLYGLYASNASN(chain 'A' and (resid 9 through 20 or (resid 21...AA9 - 201 - 12
12ILEILELYSLYS(chain 'A' and (resid 9 through 20 or (resid 21...AA31 - 4923 - 41
13ILEILEPHEPHE(chain 'A' and (resid 9 through 20 or (resid 21...AA52 - 5944 - 51
14PHEPHEASNASN(chain 'A' and (resid 9 through 20 or (resid 21...AA61 - 6953 - 61
15ASPASPTYRTYR(chain 'A' and (resid 9 through 20 or (resid 21...AA71 - 7263 - 64
16METMETGLNGLN(chain 'A' and (resid 9 through 20 or (resid 21...AA74 - 14466 - 136
17TYRTYRALAALA(chain 'A' and (resid 9 through 20 or (resid 21...AA146 - 149138 - 141
28GLYGLYASNASN(chain 'B' and (resid 9 through 34 or (resid 35...BB9 - 201 - 12
29ILEILELYSLYS(chain 'B' and (resid 9 through 34 or (resid 35...BB31 - 4923 - 41
210ILEILEPHEPHE(chain 'B' and (resid 9 through 34 or (resid 35...BB52 - 5944 - 51
211PHEPHEASNASN(chain 'B' and (resid 9 through 34 or (resid 35...BB61 - 6953 - 61
212ASPASPTYRTYR(chain 'B' and (resid 9 through 34 or (resid 35...BB71 - 7263 - 64
213METMETGLNGLN(chain 'B' and (resid 9 through 34 or (resid 35...BB74 - 14466 - 136
214TYRTYRALAALA(chain 'B' and (resid 9 through 34 or (resid 35...BB146 - 149138 - 141

NCS ensembles :
ID
1
2

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Components

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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FBF / 4-(trifluoromethyl)benzenecarboximidamide


Mass: 188.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7F3N2
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 4000, 0.1 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: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 35809 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.07 Å2 / CC1/2: 1 / Rsym value: 0.059 / Net I/σ(I): 19.06
Reflection shellResolution: 1.68→1.77 Å / Num. unique obs: 5690 / CC1/2: 0.786 / Rsym value: 0.843

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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: 1.68→24.94 Å / SU ML: 0.1817 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.0456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 1790 5 %Random selection
Rwork0.1788 33996 --
obs0.1803 35786 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.67 Å2
Refinement stepCycle: LAST / Resolution: 1.68→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 29 201 2386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872286
X-RAY DIFFRACTIONf_angle_d0.88923107
X-RAY DIFFRACTIONf_chiral_restr0.0525339
X-RAY DIFFRACTIONf_plane_restr0.0068419
X-RAY DIFFRACTIONf_dihedral_angle_d15.88791366
LS refinement shellResolution: 1.68→1.73 Å
RfactorNum. reflection% reflection
Rfree0.2714 135 -
Rwork0.2468 2557 -
obs--99.67 %
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)
10.0395070529923-0.0095369916939-0.01479449763040.0294040239162-0.05139921614230.1105058465190.198223806920.329832038453-0.0223273602442-0.03395204419650.345279516420.2631358534020.1551698037440.140748923897-8.42333916993E-50.283713632937-0.0353854410214-0.02307211096250.429784820999-0.02488798045180.38876213427-16.056490514712.6695699933186.636088506
20.139037769208-0.167817930115-0.2133021169770.3299759628970.254181046190.333610786421-0.103312002210.1881155493140.208546577804-0.201029691753-0.1883450706820.4196407958840.5850725451240.506528384957-0.01457251458290.2244464944810.0450532214687-0.02464356910260.3125793181480.004031578507030.272724196925-22.21890918328.85233865957179.962917988
30.0275462472490.0243156782131-0.008921168609310.0327424938273-0.03020461615040.03934746970860.261583938321-0.0834304680252-0.421493977586-0.0917219173764-0.0897799109833-0.001737939259220.326513039683-0.113707451721-0.0005646822151150.223723160257-0.0109696578162-0.02880972017130.265727213960.009287196473270.26474859952-32.09268051158.80492141055175.651229272
40.127074173197-0.1156154283530.02510914138430.106280848476-0.04892258233450.04579296297420.001045717435540.2269021159770.139013986426-0.3029243043950.02910452346860.0621364979424-0.287008894317-0.0854923273619-0.0001359390498690.2023110406960.0351337728928-0.02665921549570.317545783932-0.02520917439980.2381216682-39.964681974521.0566855338173.140213343
50.4281198576940.355956663752-0.1087165525020.348927755079-0.203185322680.4213672779660.04040117692120.05128785043140.04826603308950.0358937855854-0.0187214356375-0.02073162991280.0132210439672-0.09516119197655.99780023176E-50.1628341879360.01647024551360.005473515151030.2339358602820.01062095606770.193573453803-28.377635315420.7567817479174.398052819
60.04034061231330.0189004440283-0.04560207460850.0460963856877-0.01539621212970.0460968051299-0.07460450517040.048470060660.1602738912070.1877737403520.1200012105490.247603634729-0.291997277687-0.3679512745660.0003298633484160.2422453534820.0784947546570.05816407688050.3127671396630.02883861971620.276325101951-33.230368922732.819284489171.767270503
70.0120288085229-0.00445779366977-0.0193792275530.01002691066230.01361596974280.0349381317668-0.18295796356-0.3747706771490.4166901460060.2670916301580.181221930381-0.382294397263-0.2257871197640.06031717130740.0001543175257930.2382857419970.0238118688213-5.16225442517E-50.302692438494-0.0168426260930.264191085901-26.787536442135.1886988842170.260673454
80.2083800901530.1517028109750.1471045654660.2182225821570.1322869752060.112364372394-0.368793821108-0.1424191965080.0873374768299-0.0880948461522-0.162651739490.535063126728-0.8533248952630.226462972137-0.008997780644860.30729876943-0.00809835723585-0.03350620863850.448080794447-0.0407391300880.346806196755-18.760593760426.8599044672176.784833524
90.4573741741970.3937578483990.3506440983910.3209197279620.3007688284840.2706589887490.0271808648717-0.1513365071750.4771060391160.0919160890699-0.132472709128-0.165720920798-0.02517864694340.007795369960452.99945317017E-50.2476953004420.002133268202070.006986336616030.28649664904-0.01237127875730.2526919381682.8531859034535.744260502171.363105628
100.03948401177320.02120840105210.07430887491720.2481274729750.0369644738230.4903205259210.121750294061-0.116855962968-0.2581294088750.006865948919820.08466969427710.142259721270.0565948243051-0.143287986180.0005402388043770.1973680983590.00614110639949-0.0151323760020.2646536727550.01998127001070.229525536608-4.6167135802729.8313855048173.890508353
110.4143861263810.2294168029570.473077935480.3558068164320.5017215302180.745878853952-0.0537742207533-0.122261693356-0.0532397859026-0.01909171219280.105895298923-0.04228374424170.03974231712410.01071211345598.39388846112E-50.2592319097640.005741880997350.002529375050170.2278449912670.009058847323410.222996226747-6.8933476270524.4186240221165.027889222
120.0475427527056-0.0332766692274-0.001581566291230.0253828156552-0.009088510138720.03322120400530.1549267494350.007076861331350.154806505574-0.1836945443220.299659718830.04853390186320.0843303714165-0.3433836464339.63070101336E-60.437076938620.099675995106-0.07045259807970.401373608348-0.04622319185010.469602251486-13.326282846133.44859582156.674613084
130.0611025952252-0.03668937704170.06359486813870.1023812488430.01553954104390.483335105744-0.04344440430060.0868821922408-0.167364127988-0.2961836550470.2002008135470.1913012785140.473430113522-0.1909362910879.40251076417E-50.309536047171-0.0251681841541-0.01938667348330.258640025708-0.0147389817470.26108145469-8.3050556188917.6756599348155.207633454
140.09220554938940.0759880793995-0.004027141482030.0622533585213-0.02253928605750.06805423717730.141340727002-0.0856521258692-0.155553598618-0.0954583791081-0.0823463742230.3915024569050.274115338915-0.163803918916-0.0002351685125110.295239231463-0.00317652942239-0.01220887091140.2985509960390.01814553778090.25683699439-11.68987331123.2130236644147.478228585
150.55317411073-0.042149232677-0.0326349726420.0291295917512-0.07863170301770.47897858627-0.02257934922210.1874583746976.40963563584E-5-0.149613865208-0.09855689650540.1772094602220.2036016260340.443116728039-0.0001490325060430.3159289906630.05497664994310.007008978130240.2539910163130.009772175400230.250037049714-3.3417838195622.106149594145.615913115
160.51062483152-0.1593067023320.1286606539460.0465154501424-0.04460105423170.806881972532-0.0155199858172-0.06957122915260.06632718136650.1021141318790.08525715108460.0252862439250.02274780855090.1760617258867.73073998859E-50.1732314940490.007659731789810.004412884004930.2293013342290.003851027867380.216650813639-24.973339655431.186733113161.788999448
170.238222448697-0.129910509629-0.01374194308060.07031031569950.02330753810710.04030561834430.1533148058070.0783806246030.0319128142322-0.2133378403210.152002688392-0.410242458136-0.08357191205930.515305256828-0.0001682265502830.2060773367190.009120913404970.01515471284170.2830725011660.01962024665460.254847654229-22.627291392233.4002569482152.670643892
180.202720068190.04553269385690.1588802654010.1040233564940.0626265902940.1155240705820.0295938484269-0.0362244841986-0.126367802082-0.325750554969-0.0797119511583-0.1380788274110.0841520971121-0.111462003718-0.0001090300822850.2344641445820.0330359935945-0.03438612602720.254468032308-0.009933612423550.279633641481-30.983193739431.5644991357149.630994281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 39 )
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 53 )
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 78 )
6X-RAY DIFFRACTION6chain 'A' and (resid 79 through 85 )
7X-RAY DIFFRACTION7chain 'A' and (resid 86 through 89 )
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 21 )
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 68 )
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 98 )
12X-RAY DIFFRACTION12chain 'B' and (resid 99 through 103 )
13X-RAY DIFFRACTION13chain 'B' and (resid 104 through 124 )
14X-RAY DIFFRACTION14chain 'B' and (resid 125 through 134 )
15X-RAY DIFFRACTION15chain 'B' and (resid 135 through 150 )
16X-RAY DIFFRACTION16chain 'A' and (resid 90 through 121 )
17X-RAY DIFFRACTION17chain 'A' and (resid 122 through 134 )
18X-RAY DIFFRACTION18chain 'A' and (resid 135 through 150 )

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