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- PDB-5kd8: BT_4244 metallopeptidase in complex with Tn antigen. -

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Basic information

Entry
Database: PDB / ID: 5kd8
TitleBT_4244 metallopeptidase in complex with Tn antigen.
ComponentsMetallopeptidase
KeywordsHYDROLASE / O-glycopeptidase / PF13402/M60-like / O-glycan / Hydrolase.
Function / homology
Function and homology information


transmembrane transporter binding / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M60, C-terminal / : / Peptidase M60 C-terminal domain / Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / 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 ...Peptidase M60, C-terminal / : / Peptidase M60 C-terminal domain / Putative binding domain, N-terminal / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / 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 / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / NICKEL (II) ION / SERINE / Peptidase M60 domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNoach, I. / Boraston, A.B.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Recognition of protein-linked glycans as a determinant of peptidase activity.
Authors: Noach, I. / Ficko-Blean, E. / Pluvinage, B. / Stuart, C. / Jenkins, M.L. / Brochu, D. / Buenbrazo, N. / Wakarchuk, W. / Burke, J.E. / Gilbert, M. / Boraston, A.B.
History
DepositionJun 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_seq_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
A: Metallopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8278
Polymers64,2721
Non-polymers5557
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.450, 88.230, 98.650
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 / Sugars , 2 types, 2 molecules A

#1: Protein Metallopeptidase


Mass: 64272.113 Da / Num. of mol.: 1 / Fragment: UNP residues 322-857
Source method: isolated from a genetically manipulated source
Details: In complex with Tn antigen
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4244
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q89ZX7
#6: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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 , 5 types, 161 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3350, NaH2PO4, Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.984 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.3→43.72 Å / Num. obs: 34533 / % possible obs: 99.9 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KD2

5kd2


Resolution: 2.3→43.72 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.565 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.211 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1764 5.1 %RANDOM
Rwork0.19991 ---
obs0.20212 32769 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.519 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å20 Å2
2---2.63 Å20 Å2
3---4.5 Å2
Refinement stepCycle: 1 / Resolution: 2.3→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4343 0 26 155 4524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194476
X-RAY DIFFRACTIONr_bond_other_d0.0010.024079
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9356059
X-RAY DIFFRACTIONr_angle_other_deg0.77739389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32824.823226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74715754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7331516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021092
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_it3.6895.4562150
X-RAY DIFFRACTIONr_mcbond_other3.6895.4522146
X-RAY DIFFRACTIONr_mcangle_it5.5218.1742684
X-RAY DIFFRACTIONr_mcangle_other5.5228.1732683
X-RAY DIFFRACTIONr_scbond_it3.6175.6892326
X-RAY DIFFRACTIONr_scbond_other3.6155.6882326
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.698.4173376
X-RAY DIFFRACTIONr_long_range_B_refined8.16843.2595310
X-RAY DIFFRACTIONr_long_range_B_other8.16143.2425266
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 104 -
Rwork0.287 2399 -
obs--99.68 %

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