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- PDB-1cpj: CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN... -

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Entry
Database: PDB / ID: 1cpj
TitleCRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN
ComponentsCATHEPSIN B
KeywordsHYDROLASE / THIOL PROTEASE
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / thyroid hormone generation / cellular response to thyroid hormone stimulus ...Trafficking and processing of endosomal TLR / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / thyroid hormone generation / cellular response to thyroid hormone stimulus / proteoglycan binding / Neutrophil degranulation / response to dexamethasone / response to amine / decidualization / collagen catabolic process / response to glucose / response to mechanical stimulus / cysteine-type peptidase activity / skeletal muscle tissue development / collagen binding / epithelial cell differentiation / proteolysis involved in protein catabolic process / response to cytokine / peptide binding / protein catabolic process / response to organic cyclic compound / sarcolemma / response to peptide hormone / autophagy / cellular response to mechanical stimulus / melanosome / peptidase activity / spermatogenesis / neuron apoptotic process / response to ethanol / endopeptidase activity / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / proteolysis / extracellular space / extracellular region
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / : / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / : / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHuber, C.P. / Jia, Z.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex. Implications for structure-based inhibitor design.
Authors: Jia, Z. / Hasnain, S. / Hirama, T. / Lee, X. / Mort, J.S. / To, R. / Huber, C.P.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Crystallization of Recombinant Rat Cathepsin B
Authors: Lee, X. / Ahmed, F.R. / Hirama, T. / Huber, C.P. / Rose, D.R. / To, R. / Hasnain, S. / Tam, A. / Mort, J.S.
History
DepositionJul 17, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Remark 700SHEET THERE IS A BIFURCATED SHEET IN EACH MOLECULE. EACH IS REPRESENTED BY TWO SHEETS WITH SOME ...SHEET THERE IS A BIFURCATED SHEET IN EACH MOLECULE. EACH IS REPRESENTED BY TWO SHEETS WITH SOME STRANDS IN COMMON. THUS STRANDS 4, 5, 6 OF SHEETS SA1 AND SA2 ARE IDENTICAL TO STRANDS 2, 3, 4 OF SHEETS SA2 AND SB2 IN CHAINS A AND B, RESPECTIVELY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CATHEPSIN B
B: CATHEPSIN B


Theoretical massNumber of molelcules
Total (without water)56,8832
Polymers56,8832
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.090, 90.250, 62.100
Angle α, β, γ (deg.)90.00, 97.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6338, 0.7386, 0.2297), (0.7394, -0.6657, 0.1002), (0.2269, 0.1064, -0.9681)
Vector: -52.751, 88.132, 93.844)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 253 B 1 .. B 253 0.457

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Components

#1: Protein CATHEPSIN B


Mass: 28441.562 Da / Num. of mol.: 2 / Mutation: S115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CDNA / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00787, cathepsin B
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE V223A SUBSTITUTION WAS PRESENT IN THE PLASMID SUPPLIED TO DR. J. S. MORT BY DR. SHU CHAN ...THE V223A SUBSTITUTION WAS PRESENT IN THE PLASMID SUPPLIED TO DR. J. S. MORT BY DR. SHU CHAN ALTHOUGH IT IS NOT MENTIONED IN THE PAPER GIVING THE CDNA SEQUENCE. IT IS POSSIBLE THAT THIS CHANGE, ALSO WITH RESPECT TO THE ORIGINAL PROTEIN SEQUENCE FROM A PREPARATION OF PURIFIED PROTEIN, COULD REPRESENT A POLYMORPHISM BETWEEN THE STRAINS OF RAT THAT WERE USED IN EACH CASE. THE SUBSTITUTION IS NOT STRUCTURALLY IMPORTANT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.25 mg/mlcathepsin B1drop
23.27 mg/mlsynthetic propeptide1drop
320.5 %ammonium sulfate1reservoir
40.1 Msodium acetate1reservoir
51 %PEG40001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 24886 / % possible obs: 90.7 % / Rmerge(I) obs: 0.095

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Processing

Software
NameVersionClassification
SDMSdata collection
X-PLOR3model building
X-PLOR3refinement
SDMSdata reduction
X-PLOR3phasing
RefinementResolution: 2.2→8 Å / σ(F): 2
Details: RESIDUE ASN 222 OF BOTH CHAINS HAS PHI-PSI ANGLES OUTSIDE THE NORMALLY PERMITTED RANGE BECAUSE ITS SIDE CHAIN OXYGEN ATOM IS INVOLVED IN A HYDROGEN BOND WITH THE ADJACENT MAIN-CHAIN N-H 223.
RfactorNum. reflection% reflection
Rwork0.175 --
obs0.175 23373 93.9 %
Displacement parametersBiso mean: 21.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3868 0 0 190 4058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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