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- PDB-5oq2: Se-SAD structure of the functional region of Cwp19 from Clostridi... -

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Basic information

Entry
Database: PDB / ID: 5oq2
TitleSe-SAD structure of the functional region of Cwp19 from Clostridium difficile
ComponentsCwp19
KeywordsHYDROLASE / S-layer / glycoside hydrolase / TIM barrel
Function / homologyGlycosyl hydrolase-like 10 / Glycosyl hydrolase-like 10 / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / N-acetylmuramoyl-L-alanine amidase activity / Glycoside hydrolase superfamily / PHOSPHATE ION / Cwp19
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 / _citation.year
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cwp19
B: Cwp19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4875
Polymers90,2352
Non-polymers2523
Water2,450136
1
A: Cwp19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2122
Polymers45,1171
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cwp19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2743
Polymers45,1171
Non-polymers1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.280, 60.410, 105.050
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 45117.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: lytC_21, cwp19, lytC_5, SAMEA3374989_00994, SAMEA3375004_02322
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: L7PGA3, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.98 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 90% (50 mM monobasic potassium phosphate, 14% PEG 8000) 10% (20 mM xylitol, 20 mM myo-inositol, 20 mM D-fructose, 20 mM L-rhammnose monohydrate, 20 mM D-sorbitol, 100 mM BES/TEA pH 7.5, 40% pentane-1,5,-diol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→55.13 Å / Num. obs: 30986 / % possible obs: 100 % / Redundancy: 52.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.05 / Rrim(I) all: 0.26 / Net I/σ(I): 28.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 53.6 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 9.9 / Num. unique obs: 3026 / CC1/2: 0.98 / Rpim(I) all: 0.116 / Rrim(I) all: 0.603 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→55.13 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.885 / SU B: 7.948 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.267 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25411 1511 4.9 %RANDOM
Rwork0.19279 ---
obs0.19583 29462 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å20.79 Å2
2---0.05 Å20 Å2
3----1.04 Å2
Refinement stepCycle: 1 / Resolution: 2.3→55.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5788 0 14 136 5938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025955
X-RAY DIFFRACTIONr_bond_other_d0.0020.025529
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9458082
X-RAY DIFFRACTIONr_angle_other_deg0.91312762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39724.894282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64315983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0671522
X-RAY DIFFRACTIONr_chiral_restr0.0740.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021387
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_it1.4092.8352874
X-RAY DIFFRACTIONr_mcbond_other1.4012.8332873
X-RAY DIFFRACTIONr_mcangle_it2.3464.2463589
X-RAY DIFFRACTIONr_mcangle_other2.3464.2483590
X-RAY DIFFRACTIONr_scbond_it1.2472.8873081
X-RAY DIFFRACTIONr_scbond_other1.2472.8873081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1214.2624494
X-RAY DIFFRACTIONr_long_range_B_refined3.70632.0796900
X-RAY DIFFRACTIONr_long_range_B_other3.70632.0846894
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
Rfree0.301 108 -
Rwork0.225 2159 -
obs--99.91 %

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