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- PDB-8urn: Crystal structure of EscI(51-87)-linker-EtgA(18-152) fusion protein -

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Basic information

Entry
Database: PDB / ID: 8urn
TitleCrystal structure of EscI(51-87)-linker-EtgA(18-152) fusion protein
ComponentsEscI inner rod protein type III secretion system,EtgA protein
KeywordsHYDROLASE / Peptidoglycan glycosidase / type III secretion system / inner rod protein
Function / homologyType III secretion system, YscI/HrpB / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / protein secretion by the type III secretion system / Lysozyme-like domain superfamily / EtgA protein / L0038
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
Authorsvan den Akker, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI148875 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Structural insights into peptidoglycan glycosidase EtgA binding to the inner rod protein EscI of the type III secretion system via a designed EscI-EtgA fusion protein.
Authors: Boorman, J. / Zeng, X. / Lin, J. / van den Akker, F.
History
DepositionOct 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EscI inner rod protein type III secretion system,EtgA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7552
Polymers20,6591
Non-polymers961
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.629, 29.885, 74.564
Angle α, β, γ (deg.)90.00, 118.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein EscI inner rod protein type III secretion system,EtgA protein


Mass: 20659.199 Da / Num. of mol.: 1
Fragment: residues 51-87 of EscI followed by a linker and then residues 18-152 of EtgA with a C-terminal His-tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: escI, C9E67_00595, etgA / Production host: Escherichia coli (E. coli) / References: UniProt: O85634, UniProt: C7BUG6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5 and 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.01→28.5 Å / Num. obs: 14194 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.8
Reflection shellResolution: 2.01→2.082 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 905 / CC1/2: 0.709 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→28.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.87 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24472 660 4.7 %RANDOM
Rwork0.18897 ---
obs0.19145 13531 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0.01 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.01→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 5 55 1251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121238
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161210
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6421677
X-RAY DIFFRACTIONr_angle_other_deg0.4981.5822780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.83555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92510226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6943.736616
X-RAY DIFFRACTIONr_mcbond_other3.683.729615
X-RAY DIFFRACTIONr_mcangle_it4.7256.646767
X-RAY DIFFRACTIONr_mcangle_other4.7346.651768
X-RAY DIFFRACTIONr_scbond_it5.4384.426622
X-RAY DIFFRACTIONr_scbond_other5.3784.431619
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0247.834904
X-RAY DIFFRACTIONr_long_range_B_refined9.35637.621487
X-RAY DIFFRACTIONr_long_range_B_other9.35437.821478
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.061 Å
RfactorNum. reflection% reflection
Rfree0.288 39 -
Rwork0.254 876 -
obs--88.75 %

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