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- PDB-3e1x: The Crystal Structure of Apo Prostasin at 1.7 Angstroms Resolution -

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Basic information

Entry
Database: PDB / ID: 3e1x
TitleThe Crystal Structure of Apo Prostasin at 1.7 Angstroms Resolution
ComponentsProstasin
KeywordsHYDROLASE / Prostasin / ENaC / HCAP-1 / Channel Activating Protease / Cell membrane / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Transmembrane / Zymogen
Function / homology
Function and homology information


Formation of the cornified envelope / positive regulation of sodium ion transport / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSpraggon, G. / Hornsby, M. / Shipway, A. / Harris, J.L. / Lesley, S.A.
CitationJournal: Protein Sci. / Year: 2009
Title: Active site conformational changes of prostasin provide a new mechanism of protease regulation by divalent cations.
Authors: Spraggon, G. / Hornsby, M. / Shipway, A. / Tully, D.C. / Bursulaya, B. / Danahay, H. / Harris, J.L. / Lesley, S.A.
History
DepositionAug 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Prostasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7923
Polymers29,6081
Non-polymers1842
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.556, 54.071, 82.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Prostasin / Serine protease 8 / Prostasin light chain / Prostasin heavy chain


Mass: 29608.002 Da / Num. of mol.: 1 / Fragment: UNP residues 45-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS8 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q16651, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% Peg-6000 in 0.1M MES buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2006
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 26345 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 11.67
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.08 / Num. unique all: 2047 / Rsym value: 0.627 / % possible all: 76.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1eon

1eon


Resolution: 1.7→45.819 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1206 5.02 %random
Rwork0.1682 ---
obs0.1715 24014 88.68 %-
all-24014 --
Displacement parametersBiso mean: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.5038 Å20 Å20 Å2
2--3.0287 Å20 Å2
3----4.8731 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 12 199 2084
LS refinement shellResolution: 1.7→1.7 Å
RfactorNum. reflection
Rfree0.3605 86
Rwork0.2836 -
obs-1689

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