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- PDB-7nrg: Crystal structure of a shortened IpgC variant in complex with (1R... -

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Basic information

Entry
Database: PDB / ID: 7nrg
TitleCrystal structure of a shortened IpgC variant in complex with (1R)-2-amino-1-(4-fluorophenyl)ethanol
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Mg / Cl / Dimer / Shigella / Mutant / (1R)-2-amino-1-(4-fluorophenyl)ethanol
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / (1R)-2-amino-1-(4-fluorophenyl)ethanol / Chaperone protein IpgC
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Crystal structure of a shortened IpgC variant in complex with (1R)-2-amino-1-(4-fluorophenyl)ethanol
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionMar 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 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)33,35512
Polymers32,6212
Non-polymers73410
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-50 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.878, 57.878, 159.100
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
11ASPASPASNASN(chain 'A' and (resid 15 or resid 17 through 20...AA17 - 209 - 12
12ALAALATYRTYR(chain 'A' and (resid 15 or resid 17 through 20...AA23 - 4015 - 32
13TYRTYRPHEPHE(chain 'A' and (resid 15 or resid 17 through 20...AA42 - 4634 - 38
14ASNASNARGARG(chain 'A' and (resid 15 or resid 17 through 20...AA48 - 5140 - 43
15GLUGLUASNASN(chain 'A' and (resid 15 or resid 17 through 20...AA54 - 6946 - 61
16ASPASPTYRTYR(chain 'A' and (resid 15 or resid 17 through 20...AA71 - 7263 - 64
17METMETALAALA(chain 'A' and (resid 15 or resid 17 through 20...AA74 - 7766 - 69
18TYRTYRLEULEU(chain 'A' and (resid 15 or resid 17 through 20...AA80 - 9972 - 91
19ASPASPVALVAL(chain 'A' and (resid 15 or resid 17 through 20...AA103 - 13095 - 122
110GLNGLNALAALA(chain 'A' and (resid 15 or resid 17 through 20...AA132 - 149124 - 141
211ASPASPASNASN(chain 'B' and ((resid 15 and (name N or name...BB17 - 209 - 12
212ALAALATYRTYR(chain 'B' and ((resid 15 and (name N or name...BB23 - 4015 - 32
213TYRTYRPHEPHE(chain 'B' and ((resid 15 and (name N or name...BB42 - 4634 - 38
214ASNASNARGARG(chain 'B' and ((resid 15 and (name N or name...BB48 - 5140 - 43
216GLUGLUASNASN(chain 'B' and ((resid 15 and (name N or name...BB54 - 6946 - 61
217ASPASPTYRTYR(chain 'B' and ((resid 15 and (name N or name...BB71 - 7263 - 64
218METMETALAALA(chain 'B' and ((resid 15 and (name N or name...BB74 - 7766 - 69
219TYRTYRLEULEU(chain 'B' and ((resid 15 and (name N or name...BB80 - 9972 - 91
220ASPASPVALVAL(chain 'B' and ((resid 15 and (name N or name...BB103 - 13095 - 122
221GLNGLNALAALA(chain 'B' and ((resid 15 and (name N or name...BB132 - 149124 - 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) / References: UniProt: P0A2U4

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Non-polymers , 7 types, 140 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-UQB / (1R)-2-amino-1-(4-fluorophenyl)ethanol / (1~{R})-2-azanyl-1-(4-fluorophenyl)ethanol


Mass: 155.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10FNO
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 23% PEG 4000, 0.05 M TRIS (pH 7), 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: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 44125 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 20.79 Å2 / CC1/2: 1 / Rsym value: 0.054 / Net I/σ(I): 20.8
Reflection shellResolution: 1.57→1.65 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6947 / CC1/2: 0.848 / Rsym value: 0.782

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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: 1.57→47.81 Å / SU ML: 0.1166 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3199
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2047 2206 5 %
Rwork0.1819 41908 -
obs0.183 44114 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.42 Å2
Refinement stepCycle: LAST / Resolution: 1.57→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 41 130 2327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822349
X-RAY DIFFRACTIONf_angle_d0.85913197
X-RAY DIFFRACTIONf_chiral_restr0.0519349
X-RAY DIFFRACTIONf_plane_restr0.007425
X-RAY DIFFRACTIONf_dihedral_angle_d15.12461393
LS refinement shellResolution: 1.57→1.6 Å
RfactorNum. reflection% reflection
Rfree0.2646 132 -
Rwork0.2272 2504 -
obs--98.36 %
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)
10.06006768435270.0827942809919-0.2355691144180.115092839368-0.3230295654620.969881269726-0.0832754689913-0.04240256673270.0865207301177-0.146961485933-0.07448702290.477273839393-0.773452092909-0.191579818597-0.0001613901138060.2919621089490.0866798286403-0.02852555594620.277325790098-0.03952501324530.426431313094-7.6839161407340.957623322624.7752864875
20.015358756461-0.0188331711047-0.01530386069770.01391081719040.005830454866720.0255431003840.03958680282550.09749150466030.611433310776-0.216363371803-0.0184635087040.103411183787-0.520428394663-0.250313678933-0.0003778520487340.2968217121310.000311909128828-0.007007155651350.2010861049430.03054857554320.3394219508732.5707841426941.632073954920.7613067647
30.106252013063-0.1138881036-0.02993580654080.1083233926920.03147985449160.00276893454770.06829970678780.2918857000020.0885828475163-0.100376804622-0.124001250285-0.1487808192840.003933938756480.3104626092980.0001150411358390.1496376845370.014540107428-0.006754746069120.2699173727180.01119507736520.20150305834110.263131831229.531620005219.3086674326
40.3701269626050.278911340280.3352886948860.2412412856470.3592183250.4962823067740.0339234759756-0.0183226818081-0.0435126417065-0.00912878663113-0.0365110802859-0.02519633342990.02218552003610.02092871683714.34152576122E-50.115868996976-0.00177173044059-0.01431707115920.171048880476-0.006710750550960.148149359593-0.98320297102429.605179857419.812858275
50.133346942830.1208641871990.09544587487250.110364032040.0724632903970.07663739120680.0131243798705-0.126666942047-0.1434814322840.2816130061820.00189778745322-0.1057117755260.0528434846799-0.16598697312-0.003426356639540.1599540471390.0722701207089-0.02096298122830.251095928714-0.02199859445760.2071294865223.9935662921517.848514346317.4220707678
60.0267543302603-0.0197172055525-0.006558513670370.04402307629630.03659803013790.034583875312-0.1909845259450.0555252836627-0.7629054313860.3966672161880.09305824503960.153096914074-0.0735859671557-0.0562509256016-0.0001927988735850.195687867585-0.006834713005990.02987587865890.281597990081-0.01702497020180.318719663064-2.4069686978314.682977475615.0694043863
70.525396360158-0.320876857465-0.046250253390.342420341285-0.3004916459580.523550985523-0.01079156131610.174611613864-0.137221604059-0.0447293722260.0879444351569-0.0117288350194-0.0252366848323-0.05338848390970.4805651026720.0626868676256-0.001560955856460.004969918775990.142529362415-0.02820501221760.101838903379-4.2877559750319.85159217637.09220604183
80.2068846529240.0438802263141-0.1231501158170.129961758082-0.07020148097310.0745204454402-0.229217376482-0.170527372372-0.360108313895-0.09220902867490.140269432052-0.1311136495520.08743664350080.1193330677030.0004630859450260.190296823312-0.01373851126950.03363064733820.352681422150.04629675687130.266827756682-11.354221804322.193024944223.0153270871
90.01860163708570.01525519838210.01705872173810.0518104276643-0.0133195020.0258940390488-0.168724736260.0252158506341-0.301840195562-0.131057906703-0.0133846184838-0.1142311224680.138948775905-0.0559966621272-0.00031173723480.3976036298640.1038599093170.1036857215030.3330677187730.08344399719620.536268478675-16.75598345187.952345112723.2212113421
100.3691416674080.0471670230221-0.3239612231960.281106862844-0.05161509768920.2421514628330.05067029310380.171679207583-0.467783592519-0.125569196378-0.1191556673850.2768982640440.146087713473-0.396316487759-0.002554996342360.2050992497250.0122601547863-0.02290781013270.250452509364-0.04803701260370.208149755158-32.748758248415.458587957316.5008801526
110.162135486984-0.10524259241-0.06974066825220.0896810911749-0.06099409901220.491331269860.03275683019770.102089838695-0.00377156786492-0.0651145530225-0.0140143980925-0.1030593758690.00833539441267-0.00562324699569-8.35377181669E-60.1374163954010.006239591370990.008412871569190.210273754615-0.009842353606990.173151576093-24.52984139320.161216324919.4457607638
120.254957557217-0.107764429163-0.1549051446030.288939061574-0.340971475330.61664230483-0.02806331322910.03724562571620.0778472949881-0.0130796506940.0498734080265-0.04815246817380.00769335012029-0.006712334653725.15041146974E-50.162234059678-0.00158789631829-0.002708982736560.168125487604-0.006351956370240.175480525605-22.227997089125.439130542210.3580007952
130.07431082321040.004036064602990.0822468405498-0.000377883511620.00379717366210.07990417166720.3288503240210.447469558346-0.430600041332-0.0849322374007-0.1499124430290.04076399984940.237193365775-0.07339333288520.0002765958573420.3192682174380.03892816201690.0009686483887160.269892789867-0.00532731649660.31438268509-17.618473964316.76494031782.86082464753
140.0369030186344-0.1186716716310.0297547128960.103312311718-0.01364767725970.456608380189-0.04744505656940.1450435469180.193593258869-0.004812214812060.2821975767820.0286748163476-0.1313786006350.241094131640.00343998707080.22870535658-0.036805087377-0.002431869864750.2067970167270.02690141668270.213329292822-21.397846423432.20305311280.616033055682
150.1052249433260.03569019320230.05343107553750.0409928575124-0.003089778179530.03570890752090.1384603328540.4166198975070.39410606405-0.06788517669520.0235445971146-0.0666603751115-0.08586214928530.573659398288-8.87363424567E-50.25724205508-0.0150024722670.02379682780520.33628490242-0.007079300148120.215410624496-17.976679586826.9509977761-7.56453409167
160.7623590271730.16367592854-0.1144137768640.0337654335105-0.01574346868840.0367738253667-0.08384576640230.157523706235-0.359392057234-0.6120812029570.01041717010710.0255105731956-0.0686764460454-0.272831699757-0.02928822788820.3073487693090.0204321808417-0.0851382466050.218355927881-0.01128481940310.16496148803-25.895810905527.3997453887-9.38492877356
170.0979757176675-0.158605881796-0.03136973700320.4541413721070.2425662055290.2572007224220.06964891867530.478717591886-0.294623107862-0.374864745159-0.0672335469698-0.00418874925825-0.0713472037481-0.102701958015-0.0002795206660640.1988750386270.0292068004018-0.02837303497930.364732393686-0.09716868869050.232412714299-5.8448393494117.7873961197-2.16749141079
180.1374260912630.00757376449710.03238054860230.0302505134168-0.05597396764450.1653435416990.1434627270540.542311846749-0.0417007220168-0.610517309537-0.138343326716-0.275691927049-0.05612826684460.0260880970729-2.80916491405E-50.2933013295820.07185305734660.07644678320050.370114204633-0.004219299848970.2831305783062.1113246128718.6554516567-4.44093677071
190.0100593872056-0.0225047986855-0.02332562258830.05389842058020.06971999315960.09047655198110.09672075283540.3232323131550.2541747904360.2894109563520.4888928531990.7160998809670.124666581606-0.05977690747620.004250021137170.299579631389-0.09756552341930.07312555205880.5298621702370.01025989556190.6308872304-15.305725689934.70785482730.4492575691
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 'B' and (resid 9 through 25 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 33 )
10X-RAY DIFFRACTION10chain 'B' and (resid 34 through 51 )
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 68 )
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 98 )
13X-RAY DIFFRACTION13chain 'B' and (resid 99 through 103 )
14X-RAY DIFFRACTION14chain 'B' and (resid 104 through 124 )
15X-RAY DIFFRACTION15chain 'B' and (resid 125 through 134 )
16X-RAY DIFFRACTION16chain 'B' and (resid 135 through 150 )
17X-RAY DIFFRACTION17chain 'A' and (resid 122 through 134 )
18X-RAY DIFFRACTION18chain 'A' and (resid 135 through 151 )
19X-RAY DIFFRACTION19chain 'A' and (resid 15 through 23 )

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