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- PDB-6scb: Crystal structure of a shortened IpgC variant with two bound Magn... -

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Basic information

Entry
Database: PDB / ID: 6scb
TitleCrystal structure of a shortened IpgC variant with two bound Magnesium and two bound Chlorine atoms each
ComponentsChaperone protein IpgC
KeywordsCHAPERONE / IpgC / Mg / Cl / Dimer / Shigella / Mutant
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: 1.58 Å
AuthorsLey, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Crystal structure of a shortened IpgC variant with two bound Magnesium and two bound Chlorine atoms each
Authors: Ley, M. / Heine, A. / Klebe, G.
History
DepositionJul 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)32,7416
Polymers32,6212
Non-polymers1204
Water4,504250
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-51 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.554, 57.554, 159.979
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-420-

HOH

Noncrystallographic symmetry (NCS)NCS domain segments:

Dom-ID: 1 / Ens-ID: 1

Component-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRTYRTYR(chain 'A' and (resid 24 through 34 or (resid 35...AA24 - 4016 - 32
2TYRTYRLYSLYS(chain 'A' and (resid 24 through 34 or (resid 35...AA42 - 4934 - 41
3ILEILEGLUGLU(chain 'A' and (resid 24 through 34 or (resid 35...AA52 - 5344 - 45
4ALAALAASNASN(chain 'A' and (resid 24 through 34 or (resid 35...AA55 - 6947 - 61
5ASPASPTYRTYR(chain 'A' and (resid 24 through 34 or (resid 35...AA71 - 7263 - 64
6METMETLEULEU(chain 'A' and (resid 24 through 34 or (resid 35...AA74 - 7666 - 68
7ALAALAGLUGLU(chain 'A' and (resid 24 through 34 or (resid 35...AA78 - 8470 - 76
8PHEPHEGLNGLN(chain 'A' and (resid 24 through 34 or (resid 35...AA86 - 11478 - 106
9ARGARGGLUGLU(chain 'A' and (resid 24 through 34 or (resid 35...AA116 - 128108 - 120
10VALVALGLNGLN(chain 'A' and (resid 24 through 34 or (resid 35...AA130 - 144122 - 136
11TYRTYRALAALA(chain 'A' and (resid 24 through 34 or (resid 35...AA146 - 149138 - 141
12THRTHRTYRTYR(chain 'B' and (resid 24 through 28 or (resid 29...BB24 - 4016 - 32
13TYRTYRLYSLYS(chain 'B' and (resid 24 through 28 or (resid 29...BB42 - 4934 - 41
14ILEILEGLUGLU(chain 'B' and (resid 24 through 28 or (resid 29...BB52 - 5344 - 45
15ALAALAASNASN(chain 'B' and (resid 24 through 28 or (resid 29...BB55 - 6947 - 61
16ASPASPTYRTYR(chain 'B' and (resid 24 through 28 or (resid 29...BB71 - 7263 - 64
17METMETLEULEU(chain 'B' and (resid 24 through 28 or (resid 29...BB74 - 7666 - 68
18ALAALAGLUGLU(chain 'B' and (resid 24 through 28 or (resid 29...BB78 - 8470 - 76
19PHEPHEGLNGLN(chain 'B' and (resid 24 through 28 or (resid 29...BB86 - 11478 - 106
20ARGARGGLUGLU(chain 'B' and (resid 24 through 28 or (resid 29...BB116 - 128108 - 120
21VALVALGLNGLN(chain 'B' and (resid 24 through 28 or (resid 29...BB130 - 144122 - 136
22TYRTYRALAALA(chain 'B' and (resid 24 through 28 or (resid 29...BB146 - 149138 - 141

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Components

#1: Protein Chaperone protein IpgC


Mass: 16310.492 Da / Num. of mol.: 2 / Mutation: M1_E9del, D152_E154del
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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 4000, 0.05 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: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 43023 / % possible obs: 99.6 % / Redundancy: 4.89 % / Biso Wilson estimate: 18.92 Å2 / CC1/2: 0.999 / Rsym value: 0.055 / Net I/σ(I): 16.64
Reflection shellResolution: 1.58→1.66 Å / Redundancy: 4.72 % / Mean I/σ(I) obs: 2.42 / Num. unique obs: 6816 / CC1/2: 0.906 / Rsym value: 0.57 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDS1.02data reduction
XDS1.02data scaling
PHASER7.0.047phasing
PHENIX1.16refinement
Coot0.8.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gyz

3gyz


Resolution: 1.58→47.59 Å / SU ML: 0.1716 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.246
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 2138 4.98 %Random selection
Rwork0.1753 ---
obs0.1773 42965 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.67 Å2
Refinement stepCycle: LAST / Resolution: 1.58→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 4 250 2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812316
X-RAY DIFFRACTIONf_angle_d0.95093158
X-RAY DIFFRACTIONf_chiral_restr0.0537340
X-RAY DIFFRACTIONf_plane_restr0.0067419
X-RAY DIFFRACTIONf_dihedral_angle_d16.21681383
LS refinement shellResolution: 1.58→1.62 Å
RfactorNum. reflection% reflection
Rfree0.3478 134 -
Rwork0.2784 2662 -
obs--98.59 %
Refinement TLS params.Method: refined / Origin x: 45.2408293726 Å / Origin y: 23.4541568674 Å / Origin z: 10.2687086434 Å
111213212223313233
T0.154722686673 Å20.0050495730518 Å20.00242394278634 Å2-0.169768496147 Å2-0.000150334724097 Å2--0.14539227627 Å2
L0.258265056437 °20.0693939802139 °20.0773470250224 °2-0.115323643981 °20.0528293206899 °2--0.327451376145 °2
S-0.0572315953059 Å °0.012152436293 Å °0.010099663824 Å °-0.00257622342005 Å °0.0262485493261 Å °0.00396407787401 Å °-0.00810642149926 Å °0.00524691980659 Å °-1.22336368013E-5 Å °
Refinement TLS groupSelection details: all

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