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- PDB-7nhw: Crystal structure of a shortened IpgC variant in complex with chl... -

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Basic information

Entry
Database: PDB / ID: 7nhw
TitleCrystal structure of a shortened IpgC variant in complex with chlorzoxazone
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Dimer / Shigella / Mutant / Magnesium / Chlorine / Chlorzoxazone
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 / CHLORZOXAZONE / Chaperone protein IpgC
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
CitationJournal: To be published
Title: Crystal structure of a shortened IpgC variant in complex with chlorzoxazone
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionFeb 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 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)32,8866
Polymers32,6212
Non-polymers2654
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-50 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.515, 57.515, 159.526
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
11LEULEUTYRTYR(chain 'A' and (resid 25 through 28 or (resid 29...AA25 - 4017 - 32
12TYRTYRILEILE(chain 'A' and (resid 25 through 28 or (resid 29...AA42 - 5234 - 44
13GLUGLUASPASP(chain 'A' and (resid 25 through 28 or (resid 29...AA54 - 6646 - 58
14ASNASNTYRTYR(chain 'A' and (resid 25 through 28 or (resid 29...AA69 - 7261 - 64
15METMETALAALA(chain 'A' and (resid 25 through 28 or (resid 29...AA74 - 7766 - 69
16TYRTYRLEULEU(chain 'A' and (resid 25 through 28 or (resid 29...AA80 - 9972 - 91
17ASPASPILEILE(chain 'A' and (resid 25 through 28 or (resid 29...AA103 - 13195 - 123
18HISHISALAALA(chain 'A' and (resid 25 through 28 or (resid 29...AA133 - 149125 - 141
21LEULEUTYRTYR(chain 'B' and (resid 25 through 40 or resid 42...BB25 - 4017 - 32
22TYRTYRILEILE(chain 'B' and (resid 25 through 40 or resid 42...BB42 - 5234 - 44
23GLUGLUASPASP(chain 'B' and (resid 25 through 40 or resid 42...BB54 - 6646 - 58
24ASNASNTYRTYR(chain 'B' and (resid 25 through 40 or resid 42...BB69 - 7261 - 64
25METMETALAALA(chain 'B' and (resid 25 through 40 or resid 42...BB74 - 7766 - 69
26TYRTYRLEULEU(chain 'B' and (resid 25 through 40 or resid 42...BB80 - 9972 - 91
27ASPASPILEILE(chain 'B' and (resid 25 through 40 or resid 42...BB103 - 13195 - 123
28HISHISALAALA(chain 'B' and (resid 25 through 40 or resid 42...BB133 - 149125 - 141

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Components

#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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CLW / CHLORZOXAZONE / 5-CHLORO-2-BENZOXAZOLONE


Mass: 169.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4ClNO2
#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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 28 % PEG 4000, 0.1 M TRIS (pH 8.0), 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: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 24220 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 29.59 Å2 / Rsym value: 0.098 / Net I/σ(I): 21.44
Reflection shellResolution: 1.92→2.03 Å / Mean I/σ(I) obs: 3.55 / Num. unique obs: 3785 / Rsym value: 0.797 / % possible all: 99.8

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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: 1.92→26.87 Å / SU ML: 0.1852 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1209 5.01 %random selection
Rwork0.1912 22946 --
obs0.1934 24155 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.03 Å2
Refinement stepCycle: LAST / Resolution: 1.92→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 14 133 2258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062218
X-RAY DIFFRACTIONf_angle_d0.71653018
X-RAY DIFFRACTIONf_chiral_restr0.0464326
X-RAY DIFFRACTIONf_plane_restr0.0047411
X-RAY DIFFRACTIONf_dihedral_angle_d14.0341312
LS refinement shellResolution: 1.92→2 Å
RfactorNum. reflection% reflection
Rfree0.2571 131 -
Rwork0.2148 2477 -
obs--99.39 %
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)
10.0336001008138-0.0149833563074-0.005146785411830.00433804301440.00455444431447-0.0101034033473-0.1528685558310.0890309728474-0.0634250433859-0.248298120856-0.1900396068460.899688237772-0.652861231737-0.800086475533-0.0003919169175510.4268080875460.150433507269-0.06735381469660.48750547189-0.05930461598910.519804403036-7.6748762639141.145931559724.5954683982
20.00407291632775-0.0294656307167-0.004790079518610.07189394935850.02163474266880.012452644336-0.175578230318-0.4399072462350.5005488791-0.3166547806470.187733310621-0.0158891614259-0.978212094848-0.3548671686190.0005944533335440.5058899720250.0495020027187-0.03063792358320.293440971944-0.01632266760460.3395018994852.6441497683941.64109266520.774951114
30.158788629291-0.0616858387646-0.02595190877730.08876247529920.07021915775040.137989616279-0.07438240378460.3477005893160.1836669833630.261441153694-0.223642203323-0.285148676492-0.2463730945040.558797340769-0.001110790362170.284721605030.00416095088619-0.001240439811420.4061271605160.006074293125320.3190284015210.284410504129.790955817519.1213495849
40.3262584836630.4471720198020.2940655697540.4504401370230.3591971545960.2088701548120.02779028417560.0629992655740.117420425048-0.0537500460535-0.07173701404220.0836473829105-0.07448573358630.009657816406114.87438407693E-50.205156095296-0.00286368330969-0.02527800290510.259290527985-0.02160191698120.240370670809-1.4199661996129.755427507519.7294730158
50.08982999115250.02334158987380.1095690019720.0342728591337-0.05801296030780.252384422927-0.209483225025-0.588451812780.2329798587180.7566699331540.4795088354940.03406351850860.1883221441420.06504783572850.1965986961520.2861885760070.126833937531-0.04478938725210.4326679736420.001403525007530.2679406186093.6120289617917.232951331217.3223784828
60.03650892737670.00707917587568-0.002148701676950.02007461188940.01390445788580.0186734181463-0.2471755622350.12162285463-0.4205816799790.0506517973512-0.02853509419030.507188009717-0.03315360659970.115947271557-0.000800965103340.3013967114650.04267313875810.04259767056520.3789817046770.005467114146170.364898248568-2.3702727949114.523205927314.6748241554
70.221780522145-0.199987439312-0.1917162380510.111004231732-0.1993534809830.4929914305640.01095210754960.227612242398-0.219026809318-0.0646975155349-0.05057520933860.236277824527-0.0507531110331-0.198004978244-0.004219868761480.1591515657350.003080663459860.01343920056160.276279632398-0.01868138937680.228227483277-4.4813875261219.6854816536.97646734012
80.104289703794-0.318142585798-0.1561062167181.688926532770.5955569109740.3055823784240.1858230484010.403129533316-0.0527700203869-0.745064232967-0.1686172584340.2314036879960.0956740816469-0.284925369279-0.02371596244480.197582110197-0.0103802251949-0.003055481421760.455023040968-0.05309907368890.294341329071-6.4024285449117.596950286-2.65934328768
90.3084597805410.0312471138310.2236699937980.6114068094970.2292664166440.7626266854920.05756879422470.47601429358-0.144597196292-0.776858189604-0.1264479515960.0546496545881-0.07494053489770.155901447411-0.03728322770940.2766438134980.04935172723280.04749996749480.381534463395-0.02595948537140.3212104150921.8787952976618.3012547257-4.55532803107
100.05424311253570.0419087685037-0.06935195568040.0904812744272-0.07876136794040.0584608547021-0.0307524376957-0.647213625627-0.537136369265-0.01116368888680.0550572279588-0.3292289978410.5914162165450.2825295470050.0001978387951450.339930929899-0.04048244211180.0501672717980.4702765732410.03174726685230.35051699316-11.225400279721.451322292823.2428136143
11-0.000546428529035-0.00542859016871-0.002512784395640.01693811074520.03280296749190.0336139518424-0.22829533118-0.09033536500340.142516308454-0.22967320638-0.10284662015-0.5775401464520.5744098634540.331991713533-0.0004439798885540.7369910954520.3139781774150.09924632469560.7606757236670.1683559445850.674196060245-16.63369566577.451540621223.4810541732
120.2079121445560.0933301641783-0.09048276823530.05856048317650.03615077898790.1574213225060.1147903935880.235007436602-0.452354022737-0.183795107144-0.1471215239970.4355810060820.341051426639-0.5004377351969.89544699646E-50.360764486073-0.03066529733270.01368735530450.425902760286-0.03738975234350.269510817865-32.541503452714.74673247917.0195156218
130.115354879680.170346750232-0.01940097333530.158625602135-0.02210184632920.3651436710590.184364966062-0.0603121209247-0.0477967520535-0.171517653609-0.190561413001-0.0344449802420.0911433265059-0.0773545367772-0.0001128473164120.264716792611-0.02024416146230.03738411665550.28655048565-0.02786323668460.222659539348-24.330714725119.695854261619.8292653365
140.590045213124-0.09645884194430.003427476041590.115583707676-0.2281265614420.407667196459-0.109026659824-0.008564721448870.06509467637740.01546212759470.051646441069-0.1093196408360.205483153343-0.1487945620029.64940314307E-60.2619372694070.004213781158820.01419130421480.2907778634230.003242174900110.254283862102-22.621482201225.4315095210.5666968648
150.04850188613190.0004195264676820.0430776201879-0.00154401433714-0.01021540063220.06631876271880.1157672868340.361519336299-0.705586972083-0.0656230462356-0.06555592873410.03249126355990.206373789541-0.1613529226230.0002786045800540.485544635364-0.02425626895280.01747337523810.252943169414-0.0152297693760.3866666709-16.426575450116.81513997332.12177045346
160.0710459150189-0.0496197910132-0.06216687095670.0501043514746-0.07788691207620.3300748832440.002372268524140.110930124451-0.0371484649639-0.2284009266160.00921785569379-0.180786372401-0.2918029522560.06201007658110.0001175525795030.268018383627-0.03429701256310.00179313883030.3794540306420.009628310865470.282676849483-21.37021566632.12058840990.776081660772
170.240625817734-0.288359618196-0.3738393106830.6327209175030.1376838829411.110716644680.4679569225130.4923749202260.4599781770610.0925568670768-0.227846413096-1.32514494095-0.5007149341130.8710361461640.01527151506110.2609098339190.02919124998960.004380352623170.4477393989470.03292194198520.300531484175-17.654937950626.6807044175-7.18589632183
180.2500342538830.111989842649-0.1341373617320.0705876585050.06498164641530.253533956204-0.1176634257710.034942726897-0.172276987773-0.4243732570820.07768355473970.23137084429-0.0664894797129-0.716764450603-0.001196924728820.3498349725670.0690520539031-0.01549887397440.4331301394090.006276346136610.261525569933-25.574908054127.4053266686-9.18194359285
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 25 )
11X-RAY DIFFRACTION11chain 'B' and (resid 26 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 )

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