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- PDB-9grf: Crystal structure of X409 complexed to tetra-Tn-glycopeptide -

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Basic information

Entry
Database: PDB / ID: 9grf
TitleCrystal structure of X409 complexed to tetra-Tn-glycopeptide
Components
  • Metalloprotease StcE
  • tetra-Tn-glycopeptide
KeywordsSUGAR BINDING PROTEIN / Mucin binding module / mucin / O-glycans
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M66 domain / ToxR activated gene A lipoprotein domain / : / Peptidase M66 / ToxR activated gene A lipoprotein domain / Peptidase family M66 domain profile. / : / Metalloprotease StcE, beta-sandwich domain / Metalloprotease StcE, C-terminal / Beta/Gamma crystallin
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Metalloprotease StcE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsVeloz, B. / Taleb, V. / Hurtado-Guerrero, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2022-136362NB-I00 Spain
CitationJournal: Nat Commun / Year: 2025
Title: Microbial binding module employs sophisticated clustered saccharide patches to selectively adhere to mucins.
Authors: Jaroentomeechai, T. / Veloz, B. / Soares, C.O. / Goerdeler, F. / Grosso, A.S. / Bull, C. / Miller, R.L. / Furukawa, S. / Gines-Alcober, I. / Taleb, V. / Merino, P. / Ghirardello, M. / ...Authors: Jaroentomeechai, T. / Veloz, B. / Soares, C.O. / Goerdeler, F. / Grosso, A.S. / Bull, C. / Miller, R.L. / Furukawa, S. / Gines-Alcober, I. / Taleb, V. / Merino, P. / Ghirardello, M. / Companon, I. / Coelho, H. / Dias, J.S. / Vincentelli, R. / Henrissat, B. / Joshi, H. / Clausen, H. / Corzana, F. / Marcelo, F. / Hurtado-Guerrero, R. / Narimatsu, Y.
History
DepositionSep 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metalloprotease StcE
M: tetra-Tn-glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1886
Polymers12,3032
Non-polymers8854
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint20 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.696, 76.050, 27.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-965-

HOH

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Components

#1: Protein Metalloprotease StcE / Mucinase / Neutral zinc metalloprotease StcE / Secreted protease of C1 esterase inhibitor from EHEC


Mass: 11415.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The 4 glycine residues in the N-terminus come from the construct but it is not present in the theoretical sequence. This is why they have been numbered as negative numbers.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: stcE, tagA, L7031, ECO57PM83 / Production host: Escherichia coli (E. coli)
References: UniProt: O82882, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide tetra-Tn-glycopeptide


Mass: 886.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Sugar
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 51.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Polyethylene glycol monomethyl ether 5,000 Lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.14→20 Å / Num. obs: 49244 / % possible obs: 97.9 % / Redundancy: 12.4 % / CC1/2: 0.998 / Rpim(I) all: 0.014 / Net I/σ(I): 34.4
Reflection shellResolution: 1.14→1.2 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 10.2 / Num. unique obs: 6153 / CC1/2: 0.992 / Rsym value: 0.051

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→19.84 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.383 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 2002 4.1 %RANDOM
Rwork0.1562 ---
obs0.15685 47185 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.344 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0 Å2-0 Å2
2--0.51 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.14→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 0 188 1096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0151072
X-RAY DIFFRACTIONr_bond_other_d0.0040.018991
X-RAY DIFFRACTIONr_angle_refined_deg2.2471.8971478
X-RAY DIFFRACTIONr_angle_other_deg1.1321.9412318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1135115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.94155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46710147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211163
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021223
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_it0.9740.834432
X-RAY DIFFRACTIONr_mcbond_other0.9730.834432
X-RAY DIFFRACTIONr_mcangle_it1.271.49538
X-RAY DIFFRACTIONr_mcangle_other1.2711.494539
X-RAY DIFFRACTIONr_scbond_it2.051.028640
X-RAY DIFFRACTIONr_scbond_other2.0491.028641
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1011.807934
X-RAY DIFFRACTIONr_long_range_B_refined5.28916.291154
X-RAY DIFFRACTIONr_long_range_B_other4.86612.391086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 121 -
Rwork0.181 2726 -
obs--77.81 %

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