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- PDB-3h7d: The crystal structure of the cathepsin K Variant M5 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3h7d
TitleThe crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate
ComponentsCathepsin K
KeywordsHYDROLASE / glycosaminoglycan / sulfhydryl peptidase / cathepsin K mutant / ternary complex / Disease mutation / Disulfide bond / Glycoprotein / Hydrolase / Lysosome / Protease / Thiol protease / Zymogen
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 / MOLECULAR REPLACEMENT / 2.242 Å resolution
AuthorsCherney, M.M. / Kienetz, M. / Bromme, D. / James, M.N.G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure-activity analysis of cathepsin K/chondroitin 4-sulfate interactions.
Authors: Cherney, M.M. / Lecaille, F. / Kienitz, M. / Nallaseth, F.S. / Li, Z. / James, M.N. / Bromme, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 24, 2009 / Release: Apr 28, 2010
RevisionDateData content typeGroupProviderType
1.0Apr 28, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jan 15, 2014Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin K
E: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,20612
Polyers46,9192
Non-polymers2,28710
Water4,648258
1
A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3469
Polyers23,4591
Non-polymers1,8878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8603
Polyers23,4591
Non-polymers4012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cathepsin K
hetero molecules

A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,69218
Polyers46,9192
Non-polymers3,77316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area (Å2)5540
ΔGint (kcal/M)22
Surface area (Å2)19490
MethodPISA
4
E: Cathepsin K
hetero molecules

E: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7206
Polyers46,9192
Non-polymers8014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area (Å2)2530
ΔGint (kcal/M)-9
Surface area (Å2)18180
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)140.564, 42.014, 87.509
Angle α, β, γ (deg.)90.00, 94.19, 90.00
Int Tables number5
Space group name H-MC 1 2 1
Detailsmonomer

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Components

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Protein/peptide , 1 types, 2 molecules AE

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


Mass: 23459.307 Da / Num. of mol.: 2 / Fragment: UNP residues 115-329 / Mutation: K9E, I171E, Q172S, N190M, K191G, L195K / Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#3: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


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


Mass: 301.271 Da / Num. of mol.: 3 / Formula: C8H15NO9S
#5: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 2 / Formula: C15H30N5O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Formula: H2O / Water

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Details

Nonpolymer detailsTHE OLIGOSACCHARIDE CHAIN (BDP-ASG)N IS CONTINUOUS. IT IS RUNNING THROUGH THE SEVERAL UNIT CELLS. ...THE OLIGOSACCHARIDE CHAIN (BDP-ASG)N IS CONTINUOUS. IT IS RUNNING THROUGH THE SEVERAL UNIT CELLS. ONLY A HEXASACCHARIDE IN EACH ASYMMETRIC UNIT CAN BE SEEN. THERE ARE DISORDERED PARTS BETWEEN HEXASACCHARIDES THAT WERE NOT MODELED. O3 ATOM OF ASG 221 IS ALSO LACKING DENSITY TO PLACE IT CORRECTLY.

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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: 2.75 / Density percent sol: 55.21 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% MPD, 0.1M acetate buffer, 20mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 8.3.1 / Synchrotron site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Collection date: Nov 1, 2003
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 26.2 Å2 / D resolution high: 2.25 Å / D resolution low: 50 Å / Number all: 24791 / Number obs: 24692 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.133 / NetI over sigmaI: 10 / Redundancy: 3.6 % / Percent possible obs: 99.6
Reflection shellRmerge I obs: 0.535 / Highest resolution: 2.25 Å / Lowest resolution: 2.33 Å / MeanI over sigI obs: 2.5 / Redundancy: 3.4 % / Percent possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.4_4)refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATK
Overall SU ML: 0.9 / Sigma F: 1.34 / Overall phase error: 23.08
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL / Solvent model param bsol: 61.713 / Solvent model param ksol: 0.411
Displacement parametersAniso B11: 4.2954 Å2 / Aniso B12: - Å2 / Aniso B13: 2.1239 Å2 / Aniso B22: -6.4414 Å2 / Aniso B23: - Å2 / Aniso B33: 2.146 Å2
Least-squares processR factor R free: 0.2377 / R factor R work: 0.1774 / R factor obs: 0.1805 / Highest resolution: 2.242 Å / Lowest resolution: 40.245 Å / Number reflection R free: 1256 / Number reflection obs: 24685 / Percent reflection R free: 5.09 / Percent reflection obs: 99.15
Refine hist #LASTHighest resolution: 2.242 Å / Lowest resolution: 40.245 Å
Number of atoms included #LASTProtein: 3286 / Nucleic acid: 0 / Ligand: 142 / Solvent: 258 / Total: 3686
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073507
X-RAY DIFFRACTIONf_angle_d1.0734739
X-RAY DIFFRACTIONf_dihedral_angle_d18.3661332
X-RAY DIFFRACTIONf_chiral_restr0.071468
X-RAY DIFFRACTIONf_plane_restr0.008616
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.24190.31530.22712.3317128246295.00
2.33170.25600.19962.4378128256399.00
2.43780.28160.18822.5663142255899.00
2.56630.29930.18862.72701332604100.00
2.72700.22700.16862.93751472633100.00
2.93750.24250.15893.23301382622100.00
3.23300.19820.14653.70061492599100.00
3.70060.17900.13634.66121342672100.00
4.66120.24870.204540.25191572716100.00

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