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- PDB-6xt1: The structure of the M60 catalytic domain from Clostridium perfri... -

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Basic information

Entry
Database: PDB / ID: 6xt1
TitleThe structure of the M60 catalytic domain from Clostridium perfringens ZmpC in complex the sialyl T antigen
ComponentsZmpC Glycopeptidase
KeywordsHYDROLASE / glycopeptidase
Function / homology
Function and homology information


Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. ...Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like 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 / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
SERINE / F5/8 type C domain-containing protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Canadian Glycomics Network (GLYCONET) Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Molecular insights into architecturally complex glycopeptidases
Authors: Pluvinage, B. / Ficko-Blean, E. / Noach, I. / Stuart, C. / Thompson, N. / McClure, H. / Buenbrazo, N. / Wakarchuck, W. / Boraston, A.B.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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
A: ZmpC Glycopeptidase
B: ZmpC Glycopeptidase
C: ZmpC Glycopeptidase
D: ZmpC Glycopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,76828
Polymers240,9544
Non-polymers2,81424
Water9,278515
1
A: ZmpC Glycopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2086
Polymers60,2381
Non-polymers9695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-20 kcal/mol
Surface area22320 Å2
MethodPISA
2
B: ZmpC Glycopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3328
Polymers60,2381
Non-polymers1,0937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint22 kcal/mol
Surface area22360 Å2
MethodPISA
3
C: ZmpC Glycopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6768
Polymers60,2381
Non-polymers4387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-18 kcal/mol
Surface area22090 Å2
MethodPISA
4
D: ZmpC Glycopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5526
Polymers60,2381
Non-polymers3145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-22 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.615, 100.930, 119.024
Angle α, β, γ (deg.)90.000, 95.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

#1: Protein
ZmpC Glycopeptidase / F5/8 type C domain-containing protein


Mass: 60238.398 Da / Num. of mol.: 4 / Fragment: M60 catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: CP4_3468 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8UNJ8
#2: Polysaccharide beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-3[DNeup5Aca2-6]DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_a6-c2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 537 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 7.6% Tascimate, 19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.49→40 Å / Num. obs: 89691 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.051 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4505 / CC1/2: 0.899 / Rpim(I) all: 0.317 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XSZ

6xsz


Resolution: 2.49→39.07 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.328 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.628 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 4404 5.1 %RANDOM
Rwork0.2345 ---
obs0.2368 82709 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.49 Å2 / Biso mean: 41.615 Å2 / Biso min: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20.06 Å2
2--0.41 Å20 Å2
3---0.61 Å2
Refinement stepCycle: final / Resolution: 2.49→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16106 0 172 515 16793
Biso mean--59.64 37.07 -
Num. residues----2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01216628
X-RAY DIFFRACTIONr_angle_refined_deg0.7021.64422544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15752038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03424.455909
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.602152721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2981561
X-RAY DIFFRACTIONr_chiral_restr0.0550.22213
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212878
LS refinement shellResolution: 2.494→2.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 298 -
Rwork0.313 6018 -
all-6316 -
obs--94.52 %

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