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- PDB-1m6d: Crystal structure of human cathepsin F -

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Basic information

Entry
Database: PDB / ID: 1m6d
TitleCrystal structure of human cathepsin F
ComponentsCathepsin F
KeywordsHYDROLASE / papain family cysteine protease
Function / homology
Function and homology information


cathepsin F / MHC class II antigen presentation / lysosomal lumen / proteolysis involved in protein catabolic process / antigen processing and presentation of exogenous peptide antigen via MHC class II / extracellular vesicle / collagen-containing extracellular matrix / lysosome / cysteine-type endopeptidase activity / proteolysis ...cathepsin F / MHC class II antigen presentation / lysosomal lumen / proteolysis involved in protein catabolic process / antigen processing and presentation of exogenous peptide antigen via MHC class II / extracellular vesicle / collagen-containing extracellular matrix / lysosome / cysteine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / 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 ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / 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-MYP / Cathepsin F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSomoza, J.R. / Palmer, J.T. / Ho, J.D.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The crystal structure of human cathepsin F and its implications for the development of novel immunomodulators
Authors: Somoza, J.R. / Palmer, J.T. / Ho, J.D.
History
DepositionJul 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2013Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,4814
Polymers47,3152
Non-polymers1,1662
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.250, 103.260, 58.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cathepsin F / CATSF


Mass: 23657.650 Da / Num. of mol.: 2 / Mutation: N97Q, N108Q, N170Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CATF / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q9UBX1, cathepsin F
#2: Chemical ChemComp-MYP / 4-MORPHOLIN-4-YL-PIPERIDINE-1-CARBOXYLIC ACID [1-(3-BENZENESULFONYL-1-PROPYL-ALLYLCARBAMOYL)-2-PHENYLETHYL]-AMIDE


Mass: 582.754 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H42N4O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: magnesium acetate, sodium cacodylate, pEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.2 Mmagnesium acetate1reservoir
20.1 Msodium cacodylate1reservoirpH6.
325 %(w/v)PEG80001reservoir
43 mg/mlcathepsin1drop
550 mMsodium acetate1droppH4.0
61 mMEDTA1drop
7150 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 43466 / Num. obs: 43466 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.086 / Net I/σ(I): 32
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.43 / % possible all: 64.5
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. measured all: 591413 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 64.5 % / Rmerge(I) obs: 0.431

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Processing

Software
NameClassification
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F2A

1f2a


Resolution: 1.7→50 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4088 9.9 %RANDOM
Rwork0.195 ---
all0.198 ---
obs0.198 41277 93.7 %-
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.72 Å20 Å20 Å2
2---2.98 Å20 Å2
3---10.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 82 280 3684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 498 9.8 %
Rwork0.272 4565 -
obs-5063 66.6 %
Refinement
*PLUS
Highest resolution: 1.7 Å / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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