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- PDB-8pn3: Crystal structure of the HC7-Glu200Ala mutant complexed to a tetr... -

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Basic information

Entry
Database: PDB / ID: 8pn3
TitleCrystal structure of the HC7-Glu200Ala mutant complexed to a tetraglycopeptide.
Components
  • DUF3472 domain-containing protein
  • Tetraglycopeptide
KeywordsHYDROLASE / Mucinase / glycoprotease / cluster of O-glycans
Function / homology2-acetamido-2-deoxy-alpha-D-galactopyranose
Function and homology information
Biological speciesBacillus cereus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsTaleb, V. / Hurtado-Guerrero, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: Nat Catal / Year: 2024
Title: A family of di-glutamate mucin-degrading enzymes that bridges glycan hydrolases and peptidases
Authors: Narimatsu, Y. / Bull, C. / Taleb, V. / Liao, Q. / Companon, I. / Sanchez-Navarro, D. / Durbesson, F. / Vincentelli, R. / Hansen, L. / Corzana, F. / Rovira, C. / Henrissat, B. / Clausen, H. / ...Authors: Narimatsu, Y. / Bull, C. / Taleb, V. / Liao, Q. / Companon, I. / Sanchez-Navarro, D. / Durbesson, F. / Vincentelli, R. / Hansen, L. / Corzana, F. / Rovira, C. / Henrissat, B. / Clausen, H. / Joshi, H.J. / Hurtado-Guerrero, R.
History
DepositionJun 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: DUF3472 domain-containing protein
B: DUF3472 domain-containing protein
C: Tetraglycopeptide
D: Tetraglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,06717
Polymers150,9174
Non-polymers2,15013
Water15,133840
1
A: DUF3472 domain-containing protein
C: Tetraglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,63210
Polymers75,4592
Non-polymers1,1738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF3472 domain-containing protein
D: Tetraglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4367
Polymers75,4592
Non-polymers9775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.703, 91.940, 99.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 12 molecules ABCD

#1: Protein DUF3472 domain-containing protein


Mass: 74159.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: DN401_14795 / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Tetraglycopeptide


Mass: 1299.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: 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.: 8 / Source method: obtained synthetically / 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

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Non-polymers , 3 types, 845 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 8000 MES Zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.44→20 Å / Num. obs: 140966 / % possible obs: 100 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.1
Reflection shellResolution: 1.44→1.52 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 20377 / CC1/2: 0.646 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→19.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.229 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20114 5577 4 %RANDOM
Rwork0.16984 ---
obs0.17107 135297 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.001 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å2-0 Å20 Å2
2---0.38 Å2-0 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.44→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 245 840 6569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125924
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175080
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.6928082
X-RAY DIFFRACTIONr_angle_other_deg0.8161.63511947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6325699
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.9841014
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56110934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021175
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_it1.8521.6272754
X-RAY DIFFRACTIONr_mcbond_other1.8521.6272754
X-RAY DIFFRACTIONr_mcangle_it2.5442.4393443
X-RAY DIFFRACTIONr_mcangle_other2.5442.443444
X-RAY DIFFRACTIONr_scbond_it2.9151.8723170
X-RAY DIFFRACTIONr_scbond_other2.9151.8733171
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.272.7074631
X-RAY DIFFRACTIONr_long_range_B_refined5.7828.7216984
X-RAY DIFFRACTIONr_long_range_B_other5.54324.6356706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 360 -
Rwork0.277 9883 -
obs--99.97 %

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