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- PDB-2ipp: Crystal Structure of the tetragonal form of human liver cathepsin B -

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Basic information

Entry
Database: PDB / ID: 2ipp
TitleCrystal Structure of the tetragonal form of human liver cathepsin B
Components(Cathepsin B) x 2
KeywordsHYDROLASE / CATHEPSIN / CYSTEINE PROTEINASE
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization ...cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization / collagen catabolic process / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / : / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / : / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-PYRIDINETHIOL / Cathepsin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHuber, C.P. / Campbell, R.L. / Hasnain, S. / Hirama, T. / To, R.
CitationJournal: To be Published
Title: Crystal Structure of the tetragonal form of human liver cathepsin B
Authors: Huber, C.P. / Campbell, R.L. / Hasnain, S. / Hirama, T. / To, R.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin B
B: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7633
Polymers27,6522
Non-polymers1111
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-33 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.580, 85.580, 34.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein/peptide Cathepsin B


Mass: 5213.840 Da / Num. of mol.: 1 / Fragment: light chain, residues 80-126 / Source method: isolated from a natural source / Details: liver / Source: (natural) Homo sapiens (human) / References: UniProt: P07858, cathepsin B
#2: Protein Cathepsin B


Mass: 22437.910 Da / Num. of mol.: 1 / Fragment: heavy chain, residues 129-333 / Source method: isolated from a natural source / Details: liver / Source: (natural) Homo sapiens (human) / References: UniProt: P07858
#3: Chemical ChemComp-PYS / 2-PYRIDINETHIOL


Mass: 111.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5NS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 271 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: ADSC / Detector: AREA DETECTOR / Date: Jul 31, 1989
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.5 Å / Num. all: 15301 / Num. obs: 13463 / % possible obs: 99.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.102

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→8 Å / Isotropic thermal model: isotropic / σ(F): 3 /
RfactorNum. reflection
obs0.157 13463
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 7 152 2097

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