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- PDB-3fvf: The Crystal Structure of Prostasin Complexed with Camostat at 1.6... -

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Basic information

Entry
Database: PDB / ID: 3fvf
TitleThe Crystal Structure of Prostasin Complexed with Camostat at 1.6 Angstroms Resolution
ComponentsProstasin
KeywordsHYDROLASE / PROSTASIN / HCAP-1 / CHANNEL ACTIVATING PROTEASE / INHIBITOR / SERINE PROTEASE / ENAC / Cell membrane / Glycoprotein / Membrane / Protease / Secreted / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
1-[4-(hydroxymethyl)phenyl]guanidine / Prostasin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Fourier Methods / Resolution: 1.6 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
DepositionJan 15, 2009Deposition 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 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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

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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)30,0225
Polymers29,6081
Non-polymers4144
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.296, 53.752, 82.924
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, Peptidase S1 domain / Mutation: C122S,N127Q,C170S
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-1JZ / 1-[4-(hydroxymethyl)phenyl]guanidine


Mass: 165.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N3O
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG-6000 buffered with 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Apr 22, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 33631 / Num. obs: 33631 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.68 Å / Rmerge(I) obs: 0.571 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Fourier Methods / Resolution: 1.6→45.105 Å / SU ML: 0.16 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 1582 4.98 %RANDOM
Rwork0.1579 ---
all0.1596 33631 --
obs0.1596 31772 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.605 Å2 / ksol: 0.408 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→45.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 26 247 2157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65170.25081490.22022537X-RAY DIFFRACTION94
1.6517-1.71070.191200.18182691X-RAY DIFFRACTION98
1.7107-1.77920.23021380.16412726X-RAY DIFFRACTION99
1.7792-1.86020.19541280.16012727X-RAY DIFFRACTION99
1.8602-1.95820.18611530.14152700X-RAY DIFFRACTION99
1.9582-2.08090.18141490.14252744X-RAY DIFFRACTION99
2.0809-2.24160.18161490.14322764X-RAY DIFFRACTION100
2.2416-2.46720.18421460.14482757X-RAY DIFFRACTION100
2.4672-2.82410.20391610.14632768X-RAY DIFFRACTION100
2.8241-3.55790.16471440.14512822X-RAY DIFFRACTION100
3.5579-45.12280.18471450.16592954X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.541 Å / Origin y: 25.8195 Å / Origin z: 4.8861 Å
111213212223313233
T0.041 Å2-0.01 Å20.0059 Å2-0.031 Å2-0.0047 Å2--0.0802 Å2
L0.3765 °20.0692 °2-0.0361 °2-0.0811 °20.0177 °2--0.6712 °2
S0.001 Å °-0.0026 Å °0.0279 Å °0.0061 Å °-0.0066 Å °0.0138 Å °-0.0356 Å °0.0182 Å °0.0048 Å °
Refinement TLS groupSelection details: chain B

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