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- PDB-3c9e: Crystal structure of the cathepsin K : chondroitin sulfate complex. -

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Basic information

Entry
Database: PDB / ID: 3c9e
TitleCrystal structure of the cathepsin K : chondroitin sulfate complex.
ComponentsCathepsin K
KeywordsHYDROLASE / n:1 cathepsin K : chondroitin sulfate complex / "beads-on-a-string" organization / Hydrolase / Lysosome / Protease / Thiol protease
Function / homologyPeptidase C1A, papain C-terminal / Cathepsin propeptide inhibitor domain (I29) / Peptidase C1A / Cathepsin propeptide inhibitor domain (I29) / Peptidase C1A, cathepsin K / Cysteine peptidase, histidine active site / Cysteine peptidase, asparagine active site / Papain-like cysteine peptidase superfamily / Papain-like cysteine endopeptidase / Papain family cysteine protease ...Peptidase C1A, papain C-terminal / Cathepsin propeptide inhibitor domain (I29) / Peptidase C1A / Cathepsin propeptide inhibitor domain (I29) / Peptidase C1A, cathepsin K / Cysteine peptidase, histidine active site / Cysteine peptidase, asparagine active site / Papain-like cysteine peptidase superfamily / Papain-like cysteine endopeptidase / Papain family cysteine protease / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Eukaryotic thiol (cysteine) proteases asparagine active site. / Collagen degradation / Degradation of the extracellular matrix / Activation of Matrix Metalloproteinases / Trafficking and processing of endosomal TLR / MHC class II antigen presentation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / cathepsin K / negative regulation of cartilage development / intramembranous ossification / regulation of keratinocyte differentiation / endolysosome lumen / proteoglycan binding / autophagy of mitochondrion / bone resorption / fibronectin binding / cysteine-type peptidase activity / collagen catabolic process / proteolysis involved in cellular protein catabolic process / extracellular matrix disassembly / lysosomal lumen / collagen binding / lysosome / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / proteolysis / serine-type endopeptidase activity / extracellular space / nucleoplasm / extracellular region / Cathepsin K
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1.8 Å resolution
AuthorsKienetz, M. / Cherney, M.M. / James, M.N.G. / Bromme, D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The crystal and molecular structures of a cathepsin K:chondroitin sulfate complex.
Authors: Li, Z. / Kienetz, M. / Cherney, M.M. / James, M.N. / Bromme, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 15, 2008 / Release: Aug 26, 2008
RevisionDateData content typeGroupProviderType
1.0Aug 26, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelNon-polymer description / Version format compliance
1.2Feb 17, 2016Structure modelDerived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4109
Polyers23,5231
Non-polymers1,8878
Water5,585310
1
A: Cathepsin K
hetero molecules

A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,82018
Polyers47,0472
Non-polymers3,77316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area (Å2)6690
ΔGint (kcal/M)38.3
Surface area (Å2)18700
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)42.000, 143.900, 87.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC 2 2 21
DetailsAuthor states that biological assembly contains one chondroitin sulfate molecule and N cathepsin K molecules. Depending on their ratio in solution and the Chondroitin sulfate moleculat weight N can vary from 1 to 20 molecules.

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Cathepsin K / / Cathepsin O / Cathepsin X / Cathepsin O2


Mass: 23523.480 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Pichia pastoris (fungus) / References: UniProt: P43235, cathepsin K

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Non-polymers , 5 types, 318 molecules

#2: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 3 / Formula: C6H10O7 / Glucuronic acid
#3: Chemical ChemComp-ASG / 2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE


Mass: 301.271 Da / Num. of mol.: 3 / Formula: C8H15NO9S
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium
#5: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Formula: C15H30N5O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Formula: H2O / Water

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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: 2.8 / Density percent sol: 56.08 %
Crystal growTemp: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Cathepsin K:chondroitin sulfate complex was made at 1:1 ratio. Precipitant contained 30% MPD, 0.1M sodium acetate buffer, 20mM calcium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, VAPOR DIFFUSION, HANGING DROP

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Data collection

SourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Collection date: Mar 2, 2002
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 4 Å / Number all: 25031 / Number obs: 25031 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.142 / NetI over sigmaI: 7.3 / Redundancy: 4 % / Percent possible obs: 99.8
Reflection shellRmerge I obs: 0.742 / Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / MeanI over sigI obs: 1.9 / Redundancy: 4.1 % / Percent possible all: 99.7

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Processing

Software
NameVersionClassificationContact authorContact author emailLocationTypeLanguageDate
MOSFLMdata reductionA.G.W. Leslieandrew[at]mrc-lmb.cam.ac.ukhttp://www.mrc-lmb.cam.ac.uk/harry/mosflm/package
CNSrefinementAxel T. Brungeraxel.brunger[at]yale.eduhttp://cns.csb.yale.edu/v1.1/packageFortran_77
PDB_EXTRACT3.004data extractionPDBsw-help[at]rcsb.rutgers.eduhttp://pdb.rutgers.edu/software/packageC++September 10, 2007
ADSCQuantumdata collection
SCALAdata scaling
MOLREPphasing
RefineSigma F: 0
Solvent computationSolvent model param bsol: 61.68
Displacement parametersB iso mean: 17.098 Å2 / Aniso B11: 2.77 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -0.962 Å2 / Aniso B23: 0 Å2 / Aniso B33: -1.808 Å2
Least-squares processR factor R free: 0.209 / R factor R work: 0.18 / R factor obs: 0.18 / Highest resolution: 1.8 Å / Lowest resolution: 4 Å / Number reflection R free: 1210 / Number reflection all: 24920 / Number reflection obs: 24920 / Percent reflection R free: 4.8 / Percent reflection obs: 99.7
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 4 Å
Number of atoms included #LASTProtein: 1649 / Nucleic acid: 0 / Ligand: 116 / Solvent: 310 / Total: 2075
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.215
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3601.500
X-RAY DIFFRACTIONc_mcangle_it1.8332.000
X-RAY DIFFRACTIONc_scbond_it2.6442.000
X-RAY DIFFRACTIONc_scangle_it3.7932.500
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2sugar.parsugar.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5e64.pare64.top

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