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- PDB-5oq3: High resolution structure of the functional region of Cwp19 from ... -

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Basic information

Entry
Database: PDB / ID: 5oq3
TitleHigh resolution structure of the functional region of Cwp19 from Clostridium difficile
ComponentsCwp19
KeywordsHYDROLASE / S-layer / glycoside hydrolase / TIM barrel
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity
Similarity search - Function
Glycosyl hydrolase-like 10 / : / Glycosyl hydrolase-like 10 / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Cell surface protein
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBradshaw, W.J. / Kirby, J.M. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
Funding support1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K027123/1
CitationJournal: FEBS J. / Year: 2017
Title: The molecular structure of the glycoside hydrolase domain of Cwp19 from Clostridium difficile.
Authors: Bradshaw, W.J. / Kirby, J.M. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
History
DepositionAug 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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: Cwp19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0404
Polymers44,8361
Non-polymers2043
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint0 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.016, 65.639, 104.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cwp19 / N-acetylmuramoyl-L-alanine amidase LytC


Mass: 44836.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: lytC_21, cwp19, lytC_5, SAMEA3374989_00994, SAMEA3375004_02322
Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: L7PGA3, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 90% (10 mM monobasic potassium phosphate, 18% PEG 8,000) 10% (20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→65.64 Å / Num. obs: 93318 / % possible obs: 99.5 % / Redundancy: 25.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.033 / Rrim(I) all: 0.123 / Net I/σ(I): 15.4
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 23.7 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4543 / CC1/2: 0.982 / Rpim(I) all: 0.2 / Rrim(I) all: 0.704 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OQ2

5oq2


Resolution: 1.35→55.51 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.971 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.045 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17415 1916 2.1 %RANDOM
Rwork0.14906 ---
obs0.14958 91316 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.682 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2--3.26 Å2-0 Å2
3----2.14 Å2
Refinement stepCycle: 1 / Resolution: 1.35→55.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 12 385 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023036
X-RAY DIFFRACTIONr_bond_other_d0.0020.022755
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9414130
X-RAY DIFFRACTIONr_angle_other_deg0.97436439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81524.93142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56715520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4211511
X-RAY DIFFRACTIONr_chiral_restr0.1060.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213380
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02615
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_it1.7931.3441460
X-RAY DIFFRACTIONr_mcbond_other1.7661.3411459
X-RAY DIFFRACTIONr_mcangle_it2.2432.0251829
X-RAY DIFFRACTIONr_mcangle_other2.2532.0271830
X-RAY DIFFRACTIONr_scbond_it2.1071.5481576
X-RAY DIFFRACTIONr_scbond_other2.0911.5471576
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3922.2092294
X-RAY DIFFRACTIONr_long_range_B_refined3.18717.2613689
X-RAY DIFFRACTIONr_long_range_B_other2.96216.5773593
X-RAY DIFFRACTIONr_rigid_bond_restr1.88135791
X-RAY DIFFRACTIONr_sphericity_free24.7645243
X-RAY DIFFRACTIONr_sphericity_bonded9.68155849
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 116 -
Rwork0.231 6708 -
obs--100 %

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