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- PDB-1deu: CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN X: A CYSTEINE PROTEASE WI... -

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Basic information

Entry
Database: PDB / ID: 1deu
TitleCRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN X: A CYSTEINE PROTEASE WITH THE PROREGION COVALENTLY LINKED TO THE ACTIVE SITE CYSTEINE
ComponentsPROCATHEPSIN X
KeywordsHYDROLASE / CYSTEINE PROTEASE / PROCATHEPSIN X / PROREGION / PROSEGMENT
Function / homology
Function and homology information


cathepsin X / negative regulation of plasminogen activation / Cargo concentration in the ER / COPII-mediated vesicle transport / Lysosome Vesicle Biogenesis / epithelial tube branching involved in lung morphogenesis / COPII-coated ER to Golgi transport vesicle / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / cysteine-type peptidase activity ...cathepsin X / negative regulation of plasminogen activation / Cargo concentration in the ER / COPII-mediated vesicle transport / Lysosome Vesicle Biogenesis / epithelial tube branching involved in lung morphogenesis / COPII-coated ER to Golgi transport vesicle / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / cysteine-type peptidase activity / carboxypeptidase activity / endoplasmic reticulum-Golgi intermediate compartment membrane / proteolysis involved in protein catabolic process / specific granule lumen / cell cortex / cytoplasmic vesicle / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / lysosome / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Cathepsin Z / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily ...Cathepsin Z / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSivaraman, J. / Nagler, D.K. / Zhang, R. / Menard, R. / Cygler, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of human procathepsin X: a cysteine protease with the proregion covalently linked to the active site cysteine.
Authors: Sivaraman, J. / Nagler, D.K. / Zhang, R. / Menard, R. / Cygler, M.
History
DepositionNov 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROCATHEPSIN X
B: PROCATHEPSIN X


Theoretical massNumber of molelcules
Total (without water)62,3692
Polymers62,3692
Non-polymers00
Water7,710428
1
A: PROCATHEPSIN X


Theoretical massNumber of molelcules
Total (without water)31,1851
Polymers31,1851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROCATHEPSIN X


Theoretical massNumber of molelcules
Total (without water)31,1851
Polymers31,1851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PROCATHEPSIN X

B: PROCATHEPSIN X


Theoretical massNumber of molelcules
Total (without water)62,3692
Polymers62,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
Buried area3940 Å2
ΔGint-19 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.820, 84.820, 169.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROCATHEPSIN X


Mass: 31184.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UBR2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 300 mM (NH4)2SO4, 12% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.7 mg/mlprotein1drop
2300 mMammonium sulfate1reservoir
312 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.007
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Feb 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.7→45 Å / Num. all: 521645 / Num. obs: 82047 / % possible obs: 95.4 % / Observed criterion σ(I): 0.3 / Redundancy: 3.5 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.5
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.208 / Num. unique all: 7673 / % possible all: 90.7
Reflection
*PLUS
Num. measured all: 521645
Reflection shell
*PLUS
% possible obs: 90.7 %

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Processing

Software
NameClassification
Adxvdata processing
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cathepsin B (PDB code 1HUC), Reference: Musil et al EMBO.J 1991, 10, 2321-2330

1huc


Resolution: 1.7→45 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1849 2.5 %RANDOM
Rwork0.204 ---
all-82047 --
obs-74610 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.26 Å2 / ksol: 0.396221 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4193 0 0 428 4621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it0.551.5
X-RAY DIFFRACTIONc_mcangle_it0.982
X-RAY DIFFRACTIONc_scbond_it0.672
X-RAY DIFFRACTIONc_scangle_it1.082.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 270 2.4 %
Rwork0.248 10758 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2

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