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- PDB-7jtv: Structure of IMPa from Pseudomonas aeruginosa in complex with an ... -

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Basic information

Entry
Database: PDB / ID: 7jtv
TitleStructure of IMPa from Pseudomonas aeruginosa in complex with an O-glycopeptide
Components
  • GLU-ALA-PRO-SER-ALA
  • Immunomodulating metalloprotease
KeywordsPROTEIN BINDING / O-glycopeptidase / glycopeptidase / glycopeptide / Pseudomonas aeruginosa / IMPa / Peptidase_M60 / M88 peptidase / gluzincin
Function / homology
Function and homology information


negative regulation of leukocyte tethering or rolling / protein transport by the Sec complex / protein secretion by the type II secretion system / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / protein catabolic process / metallopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Immunomodulating metalloprotease N-terminal domain / Immunomodulating metalloprotease helical domain / Immunomodulating metalloprotease helical domain / Immunomodulating metalloprotease N-terminal domain / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Immunomodulating metalloprotease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsNoach, I. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)130305 Canada
CitationJournal: Glycobiology / Year: 2021
Title: Structural evidence for a proline-specific glycopeptide recognition domain in an O-glycopeptidase.
Authors: Noach, I. / Boraston, A.B.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Immunomodulating metalloprotease
A: Immunomodulating metalloprotease
E: GLU-ALA-PRO-SER-ALA
H: GLU-ALA-PRO-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,89918
Polymers195,3814
Non-polymers1,51814
Water11,980665
1
B: Immunomodulating metalloprotease
E: GLU-ALA-PRO-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2015
Polymers97,6912
Non-polymers5113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Immunomodulating metalloprotease
H: GLU-ALA-PRO-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,69813
Polymers97,6912
Non-polymers1,00711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.340, 156.500, 95.680
Angle α, β, γ (deg.)90.000, 114.310, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules BAEH

#1: Protein Immunomodulating metalloprotease / IMPa / O-glycopeptidase


Mass: 96378.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: impA, PA0572 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I5W4, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide GLU-ALA-PRO-SER-ALA


Mass: 1312.339 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) synthetic construct (others)
#3: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][<C8N1O3>]{[(1+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 677 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% polyethylene glycol 3350, 0.22 M NaH2PO4, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 88358 / % possible obs: 99.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.27 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.072 / Net I/σ(I): 7.3
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.686 / Num. unique obs: 4448 / CC1/2: 0.698 / Rpim(I) all: 0.375 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata processing
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KDW

5kdw


Resolution: 2.45→29.96 Å / SU ML: 0.3194 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1573 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2341 4347 4.92 %
Rwork0.1799 83953 -
obs0.1827 88300 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.38 Å2
Refinement stepCycle: LAST / Resolution: 2.45→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13613 0 92 665 14370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007614009
X-RAY DIFFRACTIONf_angle_d0.897119058
X-RAY DIFFRACTIONf_chiral_restr0.04862080
X-RAY DIFFRACTIONf_plane_restr0.00532516
X-RAY DIFFRACTIONf_dihedral_angle_d9.04189776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.32391300.24712776X-RAY DIFFRACTION99.05
2.48-2.510.28921430.23312786X-RAY DIFFRACTION99.36
2.51-2.540.29391240.22972767X-RAY DIFFRACTION99.69
2.54-2.570.27721380.21932828X-RAY DIFFRACTION99.46
2.57-2.60.31521360.22232811X-RAY DIFFRACTION99.56
2.6-2.640.2851790.22432730X-RAY DIFFRACTION99.73
2.64-2.680.32331390.22982794X-RAY DIFFRACTION99.39
2.68-2.720.29461590.22032794X-RAY DIFFRACTION99.8
2.72-2.760.27761620.21362769X-RAY DIFFRACTION99.83
2.76-2.80.30381420.2172822X-RAY DIFFRACTION99.66
2.8-2.850.32241450.22532764X-RAY DIFFRACTION99.73
2.85-2.90.29171620.22822844X-RAY DIFFRACTION99.83
2.9-2.960.29731760.21132751X-RAY DIFFRACTION99.63
2.96-3.020.29951560.20432775X-RAY DIFFRACTION99.63
3.02-3.090.25711310.19952811X-RAY DIFFRACTION99.63
3.09-3.160.26061580.19812776X-RAY DIFFRACTION99.36
3.16-3.240.27381170.2082806X-RAY DIFFRACTION99.35
3.24-3.320.28261350.2122823X-RAY DIFFRACTION99.23
3.32-3.420.28441200.20612789X-RAY DIFFRACTION99.32
3.42-3.530.26181340.19482810X-RAY DIFFRACTION99.33
3.53-3.660.23621250.18262816X-RAY DIFFRACTION99.26
3.66-3.80.21131310.17852805X-RAY DIFFRACTION99.06
3.8-3.980.25091480.17042792X-RAY DIFFRACTION99.06
3.98-4.190.19341880.14842745X-RAY DIFFRACTION99.22
4.19-4.450.18841560.14032773X-RAY DIFFRACTION99.46
4.45-4.790.18121440.13572842X-RAY DIFFRACTION99.33
4.79-5.270.17131200.1382834X-RAY DIFFRACTION99.76
5.27-6.030.20581350.15772847X-RAY DIFFRACTION99.93
6.03-7.570.17941770.15282791X-RAY DIFFRACTION100
7.57-29.960.13271370.13052882X-RAY DIFFRACTION99.64
Refinement TLS params.Method: refined / Origin x: -6.99880296753 Å / Origin y: -0.0725174671694 Å / Origin z: 19.2250634675 Å
111213212223313233
T0.220037784035 Å2-0.0349037110872 Å20.00965121391394 Å2-0.241316737406 Å2-0.0420998113449 Å2--0.245228085487 Å2
L0.150536220135 °2-0.106955706827 °2-0.0102214082544 °2-0.179151007579 °20.0889092507782 °2--0.165205839587 °2
S0.0179220851345 Å °-0.0416681235688 Å °0.00582899024355 Å °0.000282751713009 Å °-0.0401630070316 Å °0.0371294217198 Å °0.0229036709178 Å °-0.054673507407 Å °0.0199286821178 Å °
Refinement TLS groupSelection details: all

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