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- PDB-5j72: Cwp6 from Clostridium difficile -

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Basic information

Entry
Database: PDB / ID: 5j72
TitleCwp6 from Clostridium difficile
ComponentsPutative N-acetylmuramoyl-L-alanine amidase,autolysin cwp6
KeywordsHYDROLASE / amidase_3 / CWB2 domain / cell wall protein / S-layer
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / metal ion binding
Similarity search - Function
Putative cell wall binding repeat 2 / ell wall binding domain 2 (CWB2) / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase
Similarity search - Domain/homology
CITRIC ACID / Putative N-acetylmuramoyl-L-alanine amidase,autolysin cwp6
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsRenko, M. / Usenik, A. / Turk, D.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0048 Slovenia
Centre of Excellence CIPKeBiPOP13.1.1.2.02.0005 Slovenia
CitationJournal: Structure / Year: 2017
Title: The CWB2 Cell Wall-Anchoring Module Is Revealed by the Crystal Structures of the Clostridium difficile Cell Wall Proteins Cwp8 and Cwp6.
Authors: Usenik, A. / Renko, M. / Mihelic, M. / Lindic, N. / Borisek, J. / Perdih, A. / Pretnar, G. / Muller, U. / Turk, D.
History
DepositionApr 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Refinement description
Revision 1.2Mar 22, 2017Group: Data collection / Database references
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues ...pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative N-acetylmuramoyl-L-alanine amidase,autolysin cwp6
B: Putative N-acetylmuramoyl-L-alanine amidase,autolysin cwp6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,60119
Polymers138,6392
Non-polymers96217
Water23,9421329
1
A: Putative N-acetylmuramoyl-L-alanine amidase,autolysin cwp6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5958
Polymers69,3201
Non-polymers2757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative N-acetylmuramoyl-L-alanine amidase,autolysin cwp6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,00711
Polymers69,3201
Non-polymers68710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.357, 212.916, 84.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-703-

CA

21B-705-

NA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative N-acetylmuramoyl-L-alanine amidase,autolysin cwp6


Mass: 69319.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: genomic DNA from C. difficile
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: cwp6, CD630_27840 / Plasmid: pMCSG9 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q183L9, N-acetylmuramoyl-L-alanine amidase

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Non-polymers , 6 types, 1346 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn / Details: genomic DNA from C. difficile
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: cwp6, CD630_27840 / Plasmid: pMCSG9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: N-acetylmuramoyl-L-alanine amidase
#6: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1329 / 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: 2.98 Å3/Da / Density % sol: 58.72 % / Description: cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M trisodium citrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.111.282
SYNCHROTRONBESSY 14.120.918, 1.272, 1.283, 1.379, 1.485, 1.490
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJul 2, 2013
DECTRIS PILATUS 6M2PIXELMay 26, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.2821
20.9181
31.2721
41.2831
51.3791
61.4851
71.491
ReflectionResolution: 1.7→30 Å / Num. obs: 180746 / % possible obs: 99.5 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.9
Reflection shellRmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHASERphasing
SHELXDEmodel building
ARPmodel building
XDSdata reduction
XDSdata scaling
MAINrefinement
RefinementMethod to determine structure: SAD
Starting model: Cwp8 CWB2 trimer, 1JWQ

1jwq


Resolution: 1.7→29.85 Å / Cor.coef. Fo:Fc: 0.9677 / Cor.coef. Fo:Fc free: 0.9611 / Cross valid method: FREE KICK / σ(F): 0 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 180746 100 %NONE
Rwork0.1785 180744 --
all0.1785 ---
obs0.1785 180744 100 %-
Solvent computationSolvent model: MASK FLAT BULK SOLVENT MODEL / Bsol: -20.72 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 166.56 Å2 / Biso mean: 33.1 Å2 / Biso min: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.953 Å20 Å20 Å2
2---1.483 Å20 Å2
3---2.436 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9730 0 39 1329 11098
LS refinement shellResolution: 1.7→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3716 7890 100 %
Rwork0.3555 7890 -
all-7890 -
obs-7890 1 %

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