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- PDB-9gsm: Crystal structure of X409 complexed to tetra-core1-glycopeptide -

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Basic information

Entry
Database: PDB / ID: 9gsm
TitleCrystal structure of X409 complexed to tetra-core1-glycopeptide
Components
  • Metalloprotease StcE
  • tetra-core1-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
Metalloprotease StcE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 16, 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
B: Metalloprotease StcE
M: tetra-core1-glycopeptide
N: tetra-core1-glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,07012
Polymers24,0034
Non-polymers3,0678
Water2,306128
1
A: Metalloprotease StcE
M: tetra-core1-glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5356
Polymers12,0022
Non-polymers1,5334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metalloprotease StcE
N: tetra-core1-glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5356
Polymers12,0022
Non-polymers1,5334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.194, 38.124, 72.870
Angle α, β, γ (deg.)90.00, 99.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11116.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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-core1-glycopeptide


Mass: 884.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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.: 8 / 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
[][D-1-deoxy-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Polyethylene glycol monomethyl ether 5,000 Sodium fluoride

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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: Oct 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.75→40.35 Å / Num. obs: 24440 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.994 / Rpim(I) all: 0.091 / Net I/σ(I): 6.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3516 / CC1/2: 0.567 / Rpim(I) all: 0.733 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→40.35 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.712 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1018 4.2 %RANDOM
Rwork0.242 ---
obs0.243 23363 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20.55 Å2
2--0.14 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 200 128 1997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0151928
X-RAY DIFFRACTIONr_bond_other_d0.0040.0181778
X-RAY DIFFRACTIONr_angle_refined_deg2.162.0072642
X-RAY DIFFRACTIONr_angle_other_deg1.1272.0364148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.825198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.038510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60410266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021404
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_it1.0360.824798
X-RAY DIFFRACTIONr_mcbond_other1.0360.824798
X-RAY DIFFRACTIONr_mcangle_it1.7271.46991
X-RAY DIFFRACTIONr_mcangle_other1.7261.462992
X-RAY DIFFRACTIONr_scbond_it1.6941.2811130
X-RAY DIFFRACTIONr_scbond_other1.6931.2831131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6332.2811650
X-RAY DIFFRACTIONr_long_range_B_refined5.27811.062092
X-RAY DIFFRACTIONr_long_range_B_other5.25410.462073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 79 -
Rwork0.367 1687 -
obs--99.61 %
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)
11.42220.2852-0.32130.72040.13650.6253-0.04340.00340.01260.01680.018-0.03980.0334-0.00910.02550.0733-0.0072-0.14950.00230.00730.37375.26527.051537.566
21.3629-0.2661-0.2731.1394-0.20970.3747-0.0336-0.02190.0049-0.05940.00220.03410.02730.0020.03140.07720.0081-0.15040.0029-0.00650.365310.994424.9303-1.1702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A800 - 898
2X-RAY DIFFRACTION1M1 - 11
3X-RAY DIFFRACTION2B800 - 898
4X-RAY DIFFRACTION2N1 - 8

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