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- PDB-4ci7: The crystal structure of the cysteine protease and lectin-like do... -

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Basic information

Entry
Database: PDB / ID: 4ci7
TitleThe crystal structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer associated protein of Clostridium difficile
ComponentsCELL SURFACE PROTEIN (PUTATIVE CELL SURFACE-ASSOCIATED CYSTEINE PROTEASE)
KeywordsHYDROLASE / S-LAYER / CWP / CELL WALL PROTEIN / SURFACE PROTEIN
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 speciesCLOSTRIDIUM DIFFICILE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsBradshaw, W.J. / Kirby, J.M. / Thiyagarajan, N. / Chambers, C.J. / Davies, A.H. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The Structure of the Cysteine Protease and Lectin-Like Domains of Cwp84, a Surface Layer-Associated Protein from Clostridium Difficile
Authors: Bradshaw, W.J. / Kirby, J.M. / Thiyagarajan, N. / Chambers, C.J. / Davies, A.H. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
History
DepositionDec 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Jul 23, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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)106,30320
Polymers104,2772
Non-polymers2,02618
Water16,700927
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.910, 73.490, 125.630
Angle α, β, γ (deg.)90.00, 93.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 52138.586 Da / Num. of mol.: 2
Fragment: PROPEPTIDE, CYSTEINE PROTEASE DOMAIN, LECTIN-LIKE DOMAIN, RESIDUES 33-497
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Strain: QCD-32G58 / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: C9YQ11, cathepsin L

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Non-polymers , 5 types, 945 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 927 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSTRUCTURE IS FROM RIBOTYPE 027, REFERENCE GIVEN IS FROM RIBOTYPE 630, THE ONLY DIFFERENCES ARE THAT ...STRUCTURE IS FROM RIBOTYPE 027, REFERENCE GIVEN IS FROM RIBOTYPE 630, THE ONLY DIFFERENCES ARE THAT N450 IN 630 IS D IN 027 AND A453 IN 630 IS G IN 027. GEMBANK ID 4915160

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Description: STRUCTURE SOLVED TO 1.9 A USING SEMET MAD, THEN REFINED WITH NATIVE DATA TO 1.3 A
Crystal growpH: 8
Details: 0.2 M AMMONIUM SULPHATE, 30% (V/V) PEG 4000, PH 8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0210.9795, 0.9793, 0.9795
SYNCHROTRONDiamond I0320.9717, 0.9879
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELAug 9, 2012
DECTRIS PILATUS 6M2PIXEL
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.97171
40.98791
ReflectionResolution: 1.4→48.15 Å / Num. obs: 170213 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 16
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.2 / % possible all: 65.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
CRANKphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.4→125.39 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.38 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16909 8310 5 %RANDOM
Rwork0.13814 ---
obs0.1397 156435 90.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.361 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20 Å2-0.28 Å2
2---1.04 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.4→125.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7127 0 92 927 8146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.027696
X-RAY DIFFRACTIONr_bond_other_d0.0010.027093
X-RAY DIFFRACTIONr_angle_refined_deg1.341.95510464
X-RAY DIFFRACTIONr_angle_other_deg0.853316508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4475969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29325.423343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.904151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1321516
X-RAY DIFFRACTIONr_chiral_restr0.0940.21147
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028697
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021715
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_it1.6291.4593713
X-RAY DIFFRACTIONr_mcbond_other1.6081.4573712
X-RAY DIFFRACTIONr_mcangle_it2.0062.1954655
X-RAY DIFFRACTIONr_mcangle_other2.0062.1964656
X-RAY DIFFRACTIONr_scbond_it2.7311.7873983
X-RAY DIFFRACTIONr_scbond_other2.7311.7873983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1982.5385776
X-RAY DIFFRACTIONr_long_range_B_refined4.09913.8549710
X-RAY DIFFRACTIONr_long_range_B_other3.71613.1299218
X-RAY DIFFRACTIONr_rigid_bond_restr2.543314783
X-RAY DIFFRACTIONr_sphericity_free31.9045199
X-RAY DIFFRACTIONr_sphericity_bonded11.413515323
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 354 -
Rwork0.23 7548 -
obs--59.2 %

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