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- PDB-4d59: Clostridial Cysteine protease Cwp84 C116A after propeptide cleavage -

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Basic information

Entry
Database: PDB / ID: 4d59
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
Chem-JEF / Cell surface protein (Putative cell surface-associated cysteine protease)
Similarity search - Component
Biological speciesPEPTOCLOSTRIDIUM DIFFICILE QCD-32G58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.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)91,4746
Polymers90,1982
Non-polymers1,2764
Water8,089449
1
A: CELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7373
Polymers45,0991
Non-polymers6382
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)45,7373
Polymers45,0991
Non-polymers6382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.220, 58.421, 93.100
Angle α, β, γ (deg.)89.28, 77.96, 71.62
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, RESIDUES 92-497
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PEPTOCLOSTRIDIUM DIFFICILE QCD-32G58 (bacteria)
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H63NO10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.36 Å3/Da / Density % sol: 47.94 % / Description: NONE
Crystal growpH: 8 / Details: 20% V/V DMSO, 20 % V/V JEFFAMINE M2070, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 9, 2014
RadiationMonochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.84→55.4 Å / Num. obs: 59711 / % possible obs: 83.5 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / % possible all: 83

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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: 1.84→90.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.065 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29128 2871 4.9 %RANDOM
Rwork0.22726 ---
obs0.23043 55915 82.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.433 Å2
Baniso -1Baniso -2Baniso -3
1-5.42 Å2-0.4 Å2-1.11 Å2
2---1.7 Å20 Å2
3----3.72 Å2
Refinement stepCycle: LAST / Resolution: 1.84→90.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6350 0 18 449 6817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.026570
X-RAY DIFFRACTIONr_bond_other_d0.0010.025949
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9428926
X-RAY DIFFRACTIONr_angle_other_deg0.753313782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2665826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8425.676296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.673151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.711510
X-RAY DIFFRACTIONr_chiral_restr0.080.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021488
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_it1.6963.1063263
X-RAY DIFFRACTIONr_mcbond_other1.6953.1063263
X-RAY DIFFRACTIONr_mcangle_it2.5934.6544078
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6273.2393307
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: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 189 -
Rwork0.444 4110 -
obs--81.39 %

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