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- PDB-2fud: Human Cathepsin S with Inhibitor CRA-27566 -

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Basic information

Entry
Database: PDB / ID: 2fud
TitleHuman Cathepsin S with Inhibitor CRA-27566
Componentscathepsin S
KeywordsHYDROLASE / cysteine protease / proteinase / papain / 27566
Function / homology
Function and homology information


cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures ...cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / phagocytic vesicle / laminin binding / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / adaptive immune response / lysosome / immune response / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular region
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
Chem-CRL / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSomoza, J.R.
CitationJournal: To be Published
Title: Human Cathepsin S with Inhibitor CRA-27566
Authors: Somoza, J.R.
History
DepositionJan 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 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 S
B: cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8734
Polymers50,0122
Non-polymers8612
Water5,603311
1
A: cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4372
Polymers25,0061
Non-polymers4311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4372
Polymers25,0061
Non-polymers4311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.42, 85.42, 151.99
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number91
Space group name H-MP4122
DetailsThe biological unit is probably the monomer, or one half of the asymmetric unit.

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Components

#1: Protein cathepsin S


Mass: 25006.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25774, cathepsin S
#2: Chemical ChemComp-CRL / N-{(1R)-2-[(4-CYANO-1,1-DIOXIDOTETRAHYDRO-2H-THIOPYRAN-4-YL)AMINO]-2-OXO-1-[(TRIMETHYLSILYL)METHYL]ETHYL}MORPHOLINE-4-CARBOXAMIDE


Mass: 430.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H30N4O5SSi
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 22.5%-30% PEG 8K, 0.1 M sodium citrate (pH 5.0), 0.2 M ammonium sulfate, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.73→38.82 Å / Num. obs: 51744 / % possible obs: 87.1 % / Redundancy: 7.78 % / Χ2: 1.12 / Net I/σ(I): 5.3 / Scaling rejects: 3046
Reflection shellResolution: 1.73→1.79 Å / % possible all: 29.8

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Phasing

Phasing MRRfactor: 0.494 / Cor.coef. Fo:Fc: 0.39
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
d*TREK7.2SSIbetadata scaling
EPMR2.2phasing
CNSrefinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→38.82 Å / FOM work R set: 0.895 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4198 10 %RANDOM
Rwork0.19 ---
obs0.193 41416 99.1 %-
Displacement parametersBiso mean: 17.913 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 56 311 3717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.15
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.95-1.960.304850.261657742
1.96-1.980.271700.252666736
1.98-1.990.268790.244674753
1.99-20.209770.221708785
2-2.020.243820.228681763
2.02-2.030.253800.217720800
2.03-2.050.223860.209738824
2.05-2.070.232780.205722800
2.07-2.080.205910.19750841
2.08-2.10.253740.201725799
2.1-2.120.163750.164747822
2.12-2.140.253820.186751833
2.14-2.160.213840.179734818
2.16-2.180.198890.178730819
2.18-2.20.213850.188749834
2.2-2.220.202820.166717799
2.22-2.240.215940.173750844
2.24-2.260.214800.183734814
2.26-2.290.234700.182759829
2.29-2.310.255790.189752831
2.31-2.340.233720.177742814
2.34-2.370.219910.175743834
2.37-2.390.185920.174719811
2.39-2.420.209820.183757839
2.42-2.460.255830.188753836
2.46-2.490.213800.179739819
2.49-2.530.249840.187748832
2.53-2.560.255900.19737827
2.56-2.60.215870.182739826
2.6-2.650.217750.174751826
2.65-2.690.208780.177758836
2.69-2.740.298800.184752832
2.74-2.790.237780.201753831
2.79-2.850.235900.186754844
2.85-2.910.19840.187734818
2.91-2.980.248940.209751845
2.98-3.060.229940.192744838
3.06-3.140.163760.173763839
3.14-3.230.185800.189762842
3.23-3.330.2091000.185736836
3.33-3.450.222870.183761848
3.45-3.590.199910.184754845
3.59-3.750.165760.169773849
3.75-3.950.189740.173779853
3.95-4.20.192720.158784856
4.2-4.520.201950.17774869
4.52-4.980.1751060.179764870
4.98-5.70.246830.209796879
5.7-7.180.2361040.264791895
7.18-500.267980.25843941
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2cra2.par
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param

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