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- PDB-2vhs: Cathsilicatein, a chimera -

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Basic information

Entry
Database: PDB / ID: 2vhs
TitleCathsilicatein, a chimera
ComponentsCATHSILICATEIN
KeywordsHYDROLASE / ZYMOGEN / PROTEASE / LYSOSOME / GLYCOPROTEIN / THIOL PROTEASE / SILICA CONDENSATION
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / Collagen degradation / fibronectin binding / antigen processing and presentation / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / Attachment and Entry / positive regulation of apoptotic signaling pathway / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / adaptive immune response / lysosome / immune response / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / 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 / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFairhead, M. / Kowatz, T. / McMahon, S.A. / Carter, L.G. / Oke, M. / Johnson, K.A. / Liu, H. / Naismith, J.H. / Wal, C.F.V.D.
CitationJournal: Chem. Commun. / Year: 2008
Title: Crystal Structure and Silica Condensing Activities of Silicatein Alpha-Cathepsin L Chimeras.
Authors: Fairhead, M. / Johnson, K.A. / Kowatz, T. / Mcmahon, S.A. / Carter, L.G. / Oke, M. / Liu, H. / Naismith, J.H. / Van Der Walle, C.F.
History
DepositionNov 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATHSILICATEIN
B: CATHSILICATEIN
C: CATHSILICATEIN
D: CATHSILICATEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,64612
Polymers94,8774
Non-polymers7698
Water21,1141172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-22.2 kcal/mol
Surface area42510 Å2
MethodPQS
Unit cell
Length a, b, c (Å)56.826, 58.102, 70.209
Angle α, β, γ (deg.)105.67, 104.97, 105.05
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B1 - 301
2114A1 - 301
3114C1 - 301
4114D1 - 301

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Components

#1: Protein
CATHSILICATEIN


Mass: 23719.369 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: EXTENSIVE MUTATIONS, CUSTOM DESIGNED CHIMERA / Source: (gene. exp.) HOMO SAPIENS (human) / Description: THIS IS CHIMERA, ENGINEERED / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P07711
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1172 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 137 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 138 TO SER ...ENGINEERED RESIDUE IN CHAIN A, SER 137 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 138 TO SER ENGINEERED RESIDUE IN CHAIN A, TRP 139 TO TYR ENGINEERED RESIDUE IN CHAIN A, GLU 266 TO SER ENGINEERED RESIDUE IN CHAIN A, PRO 267 TO SER ENGINEERED RESIDUE IN CHAIN A, GLU 272 TO SER ENGINEERED RESIDUE IN CHAIN A, ASP 273 TO SER ENGINEERED RESIDUE IN CHAIN A, MET 274 TO LEU ENGINEERED RESIDUE IN CHAIN A, ASP 275 TO ASN ENGINEERED RESIDUE IN CHAIN A, GLY 277 TO ALA ENGINEERED RESIDUE IN CHAIN A, VAL 278 TO MET ENGINEERED RESIDUE IN CHAIN B, SER 137 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 138 TO SER ENGINEERED RESIDUE IN CHAIN B, TRP 139 TO TYR ENGINEERED RESIDUE IN CHAIN B, GLU 266 TO SER ENGINEERED RESIDUE IN CHAIN B, PRO 267 TO SER ENGINEERED RESIDUE IN CHAIN B, GLU 272 TO SER ENGINEERED RESIDUE IN CHAIN B, ASP 273 TO SER ENGINEERED RESIDUE IN CHAIN B, MET 274 TO LEU ENGINEERED RESIDUE IN CHAIN B, ASP 275 TO ASN ENGINEERED RESIDUE IN CHAIN B, GLY 277 TO ALA ENGINEERED RESIDUE IN CHAIN B, VAL 278 TO MET ENGINEERED RESIDUE IN CHAIN C, SER 137 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS 138 TO SER ENGINEERED RESIDUE IN CHAIN C, TRP 139 TO TYR ENGINEERED RESIDUE IN CHAIN C, GLU 266 TO SER ENGINEERED RESIDUE IN CHAIN C, PRO 267 TO SER ENGINEERED RESIDUE IN CHAIN C, GLU 272 TO SER ENGINEERED RESIDUE IN CHAIN C, ASP 273 TO SER ENGINEERED RESIDUE IN CHAIN C, MET 274 TO LEU ENGINEERED RESIDUE IN CHAIN C, ASP 275 TO ASN ENGINEERED RESIDUE IN CHAIN C, GLY 277 TO ALA ENGINEERED RESIDUE IN CHAIN C, VAL 278 TO MET ENGINEERED RESIDUE IN CHAIN D, SER 137 TO ALA ENGINEERED RESIDUE IN CHAIN D, CYS 138 TO SER ENGINEERED RESIDUE IN CHAIN D, TRP 139 TO TYR ENGINEERED RESIDUE IN CHAIN D, GLU 266 TO SER ENGINEERED RESIDUE IN CHAIN D, PRO 267 TO SER ENGINEERED RESIDUE IN CHAIN D, GLU 272 TO SER ENGINEERED RESIDUE IN CHAIN D, ASP 273 TO SER ENGINEERED RESIDUE IN CHAIN D, MET 274 TO LEU ENGINEERED RESIDUE IN CHAIN D, ASP 275 TO ASN ENGINEERED RESIDUE IN CHAIN D, GLY 277 TO ALA ENGINEERED RESIDUE IN CHAIN D, VAL 278 TO MET
Sequence detailsTHIS IS AN ENGINEERED CHIMERA

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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: 2.16 Å3/Da / Density % sol: 42.54 % / Description: NONE
Crystal growpH: 6 / Details: pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→63 Å / Num. obs: 108723 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.2
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.1 / % possible all: 74

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MHW

1mhw


Resolution: 1.5→63.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.088 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5749 5 %RANDOM
Rwork0.188 ---
obs0.19 108723 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.34 Å20.83 Å2
2--0.48 Å21.04 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.5→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 40 1172 7808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226846
X-RAY DIFFRACTIONr_bond_other_d0.0010.024600
X-RAY DIFFRACTIONr_angle_refined_deg0.9811.9489274
X-RAY DIFFRACTIONr_angle_other_deg0.7443.00411166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1945872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09324.744312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.862151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6361524
X-RAY DIFFRACTIONr_chiral_restr0.0610.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021414
X-RAY DIFFRACTIONr_nbd_refined0.1940.21428
X-RAY DIFFRACTIONr_nbd_other0.1720.24908
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23435
X-RAY DIFFRACTIONr_nbtor_other0.0830.23409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.267
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5541.55498
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60626778
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.22233181
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6844.52486
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 2805 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Bmedium positional0.30.5
2Amedium positional0.260.5
3Cmedium positional0.260.5
4Dmedium positional0.290.5
1Bmedium thermal0.282
2Amedium thermal0.242
3Cmedium thermal0.252
4Dmedium thermal0.252
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 350
Rwork0.264 6128
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9464-0.2773-0.43881.3335-0.04961.11690.10150.08110.1045-0.0798-0.0213-0.07990.01560.0673-0.0802-0.1234-0.0053-0.0103-0.1341-0.0168-0.1569-4.301-28.04817.602
23.33260.3361-0.50421.0911-0.2571.0417-0.088-0.0808-0.2427-0.06440.00160.06240.0529-0.03290.0864-0.1102-0.0189-0.0004-0.1242-0.0118-0.143110.997-7.8931.592
31.2905-0.0571-0.2391.2931-0.19130.903-0.0157-0.01410.0015-0.0330.00040.0629-0.0015-0.02780.0153-0.1306-0.0128-0.0338-0.1339-0.0136-0.169322.6647.56732.632
41.44090.1658-0.02411.3003-0.35580.99850.01930.0430.0334-0.0279-0.0196-0.03550.04670.03670.0003-0.1205-0.0128-0.0199-0.1309-0.0219-0.1727.322-12.54748.64
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 220
2X-RAY DIFFRACTION2B1 - 220
3X-RAY DIFFRACTION3C1 - 220
4X-RAY DIFFRACTION4D1 - 220

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