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- PDB-7pe0: Crystal structure of IpgC in complex with J52 -

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Basic information

Entry
Database: PDB / ID: 7pe0
TitleCrystal structure of IpgC in complex with J52
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Shigella / J52
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 / Chem-483 / Chaperone protein IpgC
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGardonyi, M. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Crystal structure of IpgC in complex with J52
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionAug 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 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)32,9025
Polymers32,6212
Non-polymers2813
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-33 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.642, 57.642, 159.612
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 24 - 149 / Label seq-ID: 16 - 141

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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 BL21(DE3) (bacteria) / References: UniProt: P0A2U4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-483 / 2-(1H-imidazol-1-yl)-N-(trans-4-methylcyclohexyl)acetamide


Mass: 221.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O
#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.: 162 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 299 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: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.601
11-K, -H, -L20.399
ReflectionResolution: 1.5→47.64 Å / Num. obs: 50323 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC1/2: 1 / Rsym value: 0.054 / Net I/σ(I): 19.78
Reflection shellResolution: 1.5→1.58 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7975 / CC1/2: 0.873 / Rsym value: 0.879

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Coot0.8.9model building
XDS1.02data reduction
XDS1.02data scaling
PHASER7.0.047phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6scb

6scb


Resolution: 1.5→47.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.487 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2621 5.2 %RANDOM
Rwork0.1736 ---
obs0.1743 47701 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.14 Å2 / Biso mean: 29.19 Å2 / Biso min: 21.93 Å2
Baniso -1Baniso -2Baniso -3
1-21.44 Å20 Å20 Å2
2--21.44 Å20 Å2
3----42.89 Å2
Refinement stepCycle: final / Resolution: 1.5→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 18 162 2299
Biso mean--33.23 36.68 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192294
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.9423125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.555292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01424.955111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10315365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.449157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021818
Refine LS restraints NCS

Ens-ID: 1 / Number: 8674 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.5→1.54 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.305 174 -
Rwork0.258 3453 -
obs--98.83 %
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)
18.46751.5081-0.98950.769-0.92512.9113-0.053-0.10780.0024-0.00450.0208-0.17370.07230.30010.03220.16540.03840.0060.17050.00380.35347.7159-40.809424.8334
23.9024-2.42553.88086.3234-0.36464.73320.2626-0.1931-0.2638-0.0596-0.02770.20240.3296-0.2497-0.23480.18-0.01230.02440.12270.0070.3188-2.6349-41.382320.6619
33.0529-2.5072-0.155.26212.89232.50330.18070.1632-0.0984-0.1799-0.18940.15070.0001-0.19110.00870.0273-0.04340.00120.19680.02350.2737-10.0722-29.459418.9525
42.2190.5679-0.92870.2072-0.64533.1311-0.03840.0174-0.0258-0.0430.00180.0030.2432-0.02780.03660.0198-0.00310.01080.06370.01160.27390.7339-29.702820.0902
54.12010.56641.85894.86211.51356.1859-0.0543-0.08560.24030.43630.13510.1071-0.2808-0.3169-0.08080.0710.05110.02140.14070.01160.2668-3.4961-17.335617.4227
63.1802-0.76812.649613.3972-1.46152.2624-0.1796-0.11340.15310.14920.0606-0.2341-0.1707-0.10220.1190.09030.02140.01780.14720.00420.24322.3527-14.608714.8376
71.815-0.54370.53071.1836-1.31223.4094-0.0423-0.02330.0713-0.0570.0672-0.0411-0.07020.052-0.02490.0163-0.0101-0.01130.07440.00270.27974.509-19.47677.1155
82.2498-1.6882-0.82125.87122.87464.80110.03870.20240.1264-0.2651-0.0046-0.1985-0.31380.1437-0.03410.0235-0.00520.00310.09470.0240.28256.1639-17.5975-2.2126
90.6206-0.4874-0.09558.17840.77781.8641-0.01580.06960.1026-0.27390.04280.1212-0.0761-0.1297-0.0270.06410.0155-0.03460.15210.00380.2676-1.9926-18.5219-4.3266
105.01451.26850.79272.0911-1.01851.7303-0.0249-0.3613-0.09430.17520.06540.1713-0.27070.0425-0.04050.0467-0.014-0.01930.14910.00270.276910.7158-23.618722.4731
116.17173.2063-2.83232.5525-1.85654.0223-0.10630.20260.1468-0.13920.00050.0719-0.0961-0.28050.10570.21550.064-0.00190.1624-0.00040.36215.427-9.413724.7699
124.2114-2.00080.86314.2623-0.58732.099-0.00150.10520.2705-0.13490.0245-0.1274-0.25460.274-0.0230.0732-0.03820.00580.12290.02150.265332.589-14.615117.0469
134.6877-0.24881.42730.4654-0.06843.61750.0464-0.0399-0.0347-0.0536-0.0180.034-0.11760.0345-0.02840.0211-0.029-0.01840.09510.01440.24624.2581-19.57319.8354
142.20380.09260.45893.11251.26813.4911-0.0446-0.0057-0.05120.07140.0579-0.1293-0.02730.2034-0.01320.00420.00470.00720.09620.0080.272422.8073-25.725510.4576
153.72930.2917-4.97194.6452-3.63338.92640.4720.19730.41190.0995-0.0075-0.0267-0.7237-0.2543-0.46450.18370.0145-0.01990.1469-0.00540.314116.279-16.96472.3075
161.18640.00021.02014.2713-1.18763.6020.02030.054-0.18810.04650.03780.04810.3460.1063-0.05810.0686-0.0030.02480.0806-0.01420.310121.2872-31.89420.6393
171.9506-2.21290.67285.4482-1.99065.26390.15690.2032-0.154-0.2631-0.13080.2930.4449-0.1714-0.02610.0602-0.0318-0.00990.1236-0.02340.306217.3467-26.8408-7.3703
182.091-0.20540.74375.5686-1.23114.4445-0.07020.0157-0.1821-0.10450.127-0.06410.24790.1349-0.05680.07160.01170.02580.1268-0.00240.294825.6865-27.21-9.1636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 32
2X-RAY DIFFRACTION2A33 - 39
3X-RAY DIFFRACTION3A40 - 53
4X-RAY DIFFRACTION4A54 - 78
5X-RAY DIFFRACTION5A79 - 85
6X-RAY DIFFRACTION6A86 - 89
7X-RAY DIFFRACTION7A90 - 121
8X-RAY DIFFRACTION8A122 - 134
9X-RAY DIFFRACTION9A135 - 151
10X-RAY DIFFRACTION10B9 - 21
11X-RAY DIFFRACTION11B22 - 33
12X-RAY DIFFRACTION12B34 - 51
13X-RAY DIFFRACTION13B52 - 68
14X-RAY DIFFRACTION14B69 - 98
15X-RAY DIFFRACTION15B99 - 103
16X-RAY DIFFRACTION16B104 - 124
17X-RAY DIFFRACTION17B125 - 134
18X-RAY DIFFRACTION18B135 - 150

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