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

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Basic information

Entry
Database: PDB / ID: 6xsz
TitleThe structure of the M60 catalytic domain from Clostridium perfringens ZmpC
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
F5/8 type C domain-containing protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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)242,64331
Polymers240,9544
Non-polymers1,68927
Water16,934940
1
A: ZmpC Glycopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6147
Polymers60,2381
Non-polymers3766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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
MethodPISA
3
C: 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
MethodPISA
4
D: ZmpC Glycopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,80010
Polymers60,2381
Non-polymers5629
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.694, 99.991, 118.587
Angle α, β, γ (deg.)90.000, 95.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 60238.398 Da / Num. of mol.: 4 / Fragment: Peptidase M60 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: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 940 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.18 %
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: Aug 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. obs: 121176 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.036 / Net I/σ(I): 17.9
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / Num. unique obs: 6024 / CC1/2: 0.796 / Rpim(I) all: 0.342 / % 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: 5KDN

5kdn


Resolution: 2.25→38.98 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.904 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 5723 4.9 %RANDOM
Rwork0.2009 ---
obs0.2031 110517 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.5 Å2 / Biso mean: 36.199 Å2 / Biso min: 16.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-0.08 Å2
2--0.57 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2.25→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16029 0 96 940 17065
Biso mean--42.84 36.19 -
Num. residues----2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01216518
X-RAY DIFFRACTIONr_angle_refined_deg0.9941.64122400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61252048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57324.406901
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.612152683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5541563
X-RAY DIFFRACTIONr_chiral_restr0.0870.22184
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212858
LS refinement shellResolution: 2.25→2.306 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.303 301 -
Rwork0.248 6106 -
obs--72.31 %

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