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- PDB-4d5a: Clostridial Cysteine protease Cwp84 C116A after propeptide cleavage -

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Basic information

Entry
Database: PDB / ID: 4d5a
TitleClostridial Cysteine protease Cwp84 C116A after propeptide cleavage
ComponentsCELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE)
KeywordsHYDROLASE / S-LAYER / SURFACE LAYER
Function / homology
Function and homology information


cysteine-type peptidase activity / metal ion binding
Similarity search - Function
Lectin-like domain / Lectin like domain / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Cell surface protein (Putative cell surface-associated cysteine protease)
Similarity search - Component
Biological speciesPEPTOCLOSTRIDIUM DIFFICILE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBradshaw, W.J. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Cwp84, a Clostridium Difficile Cysteine Protease, Exhibits Conformational Flexibility in the Absence of its Propeptide
Authors: Bradshaw, W.J. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
History
DepositionNov 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE)
B: CELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,92818
Polymers90,1982
Non-polymers1,73016
Water14,250791
1
A: CELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,41412
Polymers45,0991
Non-polymers1,31611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5136
Polymers45,0991
Non-polymers4155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.094, 70.152, 78.852
Angle α, β, γ (deg.)65.22, 89.89, 80.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE) / CWP84


Mass: 45098.867 Da / Num. of mol.: 2
Fragment: CYSTEINE PROTEASE DOMAIN, LECTIN-LIKE DOMAIN, UNP RESIDUES 92-497
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PEPTOCLOSTRIDIUM DIFFICILE (bacteria) / Strain: QCD-32G58 / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9YQ11, cathepsin L
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSTRUCTURE CONSISTS OF RESIDUES 92-497 WITH C116A. THE SIGNAL PEPTIDE (1-32) AND CELL WALL BINDING ...STRUCTURE CONSISTS OF RESIDUES 92-497 WITH C116A. THE SIGNAL PEPTIDE (1-32) AND CELL WALL BINDING DOMAINS (498- 803) WERE NOT PRESENT IN THE CONSTRUCT, THE PROPEPTIDE (33- 91) WAS CLEAVED BEFORE CRYSTALISATION.

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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: 2.63 Å3/Da / Density % sol: 53.32 % / Description: NONE
Crystal growpH: 8
Details: 0.18 M NACL, 90 MM TRIS PH 8.0, 18% PEG 6000, 0.02% W/V 1,4-DIAMINOBUTANE, 0.02% W/V CYSTAMINE DIHYDROCHLORIDE, 0.02% W/V DILOXANIDE FUROATE, 0.02% W/V SARCOSINE, 0.02% W/V SPERMINE, 2MM SODIUM HEPES PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2014
RadiationMonochromator: DOUBLE SILICON CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→47.3 Å / Num. obs: 110175 / % possible obs: 90.8 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / % possible all: 49.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CI7

4ci7


Resolution: 1.6→71.38 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.026 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21055 5261 4.8 %RANDOM
Rwork0.18112 ---
obs0.18252 104911 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.346 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-0.17 Å20.15 Å2
2--1.46 Å2-0.53 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.6→71.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6350 0 69 791 7210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026927
X-RAY DIFFRACTIONr_bond_other_d0.0010.026383
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.959451
X-RAY DIFFRACTIONr_angle_other_deg0.734314860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29125.584308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45151188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0691514
X-RAY DIFFRACTIONr_chiral_restr0.0780.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021574
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_it0.8991.3923374
X-RAY DIFFRACTIONr_mcbond_other0.8951.3913373
X-RAY DIFFRACTIONr_mcangle_it1.5522.0854248
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0621.5383553
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 231 -
Rwork0.248 4376 -
obs--51.45 %

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