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- PDB-7pef: Crystal structure of IpgC in complex with DMSO -

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Basic information

Entry
Database: PDB / ID: 7pef
TitleCrystal structure of IpgC in complex with DMSO
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Shigella / DMSO
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 / Chaperone protein IpgC
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 DMSO
Authors: Gardonyi, M. / Heine, A. / Klebe, G.
History
DepositionAug 10, 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)32,7946
Polymers32,6212
Non-polymers1734
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-43 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.477, 57.477, 159.515
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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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.: 170 / 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: 47.25 %
Crystal growTemperature: 293 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: 14.2 / Wavelength: 0.8266 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.548
11-h,-k,l20.452
ReflectionResolution: 1.54→50 Å / Num. obs: 46180 / % possible obs: 99.7 % / Redundancy: 9.7 % / CC1/2: 1 / Rsym value: 0.063 / Net I/σ(I): 19.9
Reflection shellResolution: 1.54→1.62 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7299 / CC1/2: 0.891 / Rsym value: 0.89

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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: 1.54→47.52 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.423 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2261 4.9 %RANDOM
Rwork0.1613 ---
obs0.1624 43918 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.59 Å2 / Biso mean: 25.77 Å2 / Biso min: 18.52 Å2
Baniso -1Baniso -2Baniso -3
1-19.87 Å20 Å20 Å2
2--19.87 Å20 Å2
3----39.74 Å2
Refinement stepCycle: final / Resolution: 1.54→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 11 170 2349
Biso mean--27.45 30.67 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022252
X-RAY DIFFRACTIONr_bond_other_d0.0010.022117
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.9533053
X-RAY DIFFRACTIONr_angle_other_deg0.8933.0034798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6425276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66325.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31615370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.432156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
Refine LS restraints NCS

Ens-ID: 1 / Number: 8492 / 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: 1.54→1.58 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.316 153 -
Rwork0.248 3133 -
obs--98.09 %
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)
18.96770.06050.86761.99970.13293.3888-0.1197-0.090.1125-0.06220.0334-0.28130.05570.14930.08630.15670.0378-0.00270.13790.00360.3097.7672-40.254124.8281
26.3659-2.36322.34824.57641.22582.05980.0899-0.2478-0.35710.12780.00990.15170.1496-0.1361-0.09980.2005-0.0040.03430.1429-0.00210.2916-2.3313-41.25621.0748
33.8715-2.1438-0.5215.48852.3491.71540.12480.1866-0.09180.0735-0.13060.14320.0895-0.25310.00580.0551-0.01520.00760.16230.01470.2504-9.9891-29.355619.0284
41.68290.7665-0.42160.5644-0.98973.0606-0.00440.0073-0.0092-0.0157-0.0074-0.00650.05180.03970.01180.00110.00350.00670.07260.00450.26321.5276-29.554919.8673
53.98150.55991.32931.9682-2.04076.9538-0.0158-0.11660.06720.16280.12840.1545-0.0756-0.3948-0.11270.06360.0290.0150.13860.00290.2624-3.9265-17.848217.5216
61.2411-3.89061.791412.1996-5.61482.5896-0.0471-0.00530.0360.12550.0168-0.0985-0.0851-0.00720.03030.16370.0033-0.00270.1465-0.00490.26782.2296-14.294715.0323
71.5312-0.43110.29661.5529-0.70522.4616-0.0452-0.03320.09130.06140.0587-0.0129-0.0401-0.0631-0.01350.0049-0.0087-0.00550.07590.01220.27334.5295-18.82617.217
80.9977-1.8046-1.21085.18762.49994.60690.1060.15530.1708-0.4242-0.0084-0.1777-0.36180.0833-0.09760.058-0.0282-0.00910.12810.03510.27896.1939-16.8923-1.7951
90.5336-0.9934-0.3878.36091.37791.36690.00780.09650.0786-0.1190.00980.06570.0099-0.1119-0.01750.08020.0099-0.02520.15210.00620.2558-2.0945-18.8603-4.1886
106.4542.038-0.24241.1658-1.44943.6510.1468-0.34840.0230.0965-0.08990.0352-0.12680.0512-0.05680.04170.0263-0.01210.21550.01510.266711.1103-23.971222.1371
115.81552.1187-4.5071.3746-1.27314.8869-0.06630.37490.3024-0.10660.09010.3774-0.0628-0.2484-0.02380.24630.0715-0.01290.2152-0.00790.383615.2068-9.461224.8817
124.4873-2.72480.52123.9563-0.31922.71580.0235-0.01670.2253-0.07010.0219-0.2044-0.12750.208-0.04540.1045-0.02730.00780.12290.01220.262332.6789-14.70217.3992
134.673-0.03061.14880.8224-0.3722.93970.0425-0.0677-0.1169-0.0045-0.00280.0187-0.01240.0335-0.03970.0721-0.0193-0.00880.09330.00710.234124.8305-19.849619.9703
142.33630.48540.20142.09541.40923.0269-0.0481-0.0418-0.02770.10810.0515-0.1253-0.0040.2178-0.00350.0116-0.00180.00140.07910.00440.266423.0217-25.520510.694
153.4595-1.7515.95018.7823-0.672710.9662-0.2414-0.19990.0910.418-0.02380.3546-0.4349-0.47060.26530.31970.15930.01130.230.01040.298214.945-16.47993.0366
161.02-0.43510.60554.6732-0.19112.24560.0360.0807-0.1632-0.0254-0.008-0.02580.31560.1347-0.0280.0797-0.01560.01890.1062-0.01250.257520.9485-32.310.4605
173.6264-1.20071.07534.0223-1.58284.49030.11650.1686-0.0511-0.3134-0.04780.29120.2673-0.2059-0.06870.0766-0.01-0.00380.1207-0.02290.257117.2766-26.5817-7.2146
182.0173-0.54440.67885.7309-0.26423.9981-0.0150.0928-0.14940.0001-0.0148-0.07270.20470.19660.02980.07570.01020.02080.1350.00260.257125.5043-27.0402-8.8505
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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