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- PDB-3dfj: Crystal structure of human Prostasin -

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Basic information

Entry
Database: PDB / ID: 3dfj
TitleCrystal structure of human Prostasin
ComponentsProstasin
KeywordsHYDROLASE / prostasin / serine protease / Glycoprotein / Membrane / 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 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 / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsSu, H.P. / Rickert, K.W. / Darke, P.L. / Munshi, S.K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of human prostasin, a target for the regulation of hypertension.
Authors: Rickert, K.W. / Kelley, P. / Byrne, N.J. / Diehl, R.E. / Hall, D.L. / Montalvo, A.M. / Reid, J.C. / Shipman, J.M. / Thomas, B.W. / Munshi, S.K. / Darke, P.L. / Su, H.P.
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4603
Polymers28,3891
Non-polymers712
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.988, 56.241, 82.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Prostasin / Serine protease 8


Mass: 28388.748 Da / Num. of mol.: 1
Fragment: Serine protease domain of prostasin heavy chain: Residues 45-289
Mutation: C154S, C203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS8 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q16651, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.8
Details: 100mM Bis-Tris pH 5.8, 21-26% PEG 3350, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 44561 / % possible obs: 99.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.053 / Χ2: 1.011 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.45-1.53.40.3342631.03996.9
1.5-1.564.20.25644271.04199.9
1.56-1.634.20.1843871.036100
1.63-1.724.20.13844801.00999.9
1.72-1.834.30.10444460.99699.9
1.83-1.974.30.07544410.97699.8
1.97-2.174.40.0644580.99499.9
2.17-2.484.50.05444721.02799.7
2.48-3.124.50.0445310.98199.2
3.12-5040.04146561.02298

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→46.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.869 / SU B: 2.607 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2253 5.1 %RANDOM
Rwork0.19 ---
obs0.191 44493 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.37 Å2 / Biso mean: 17.362 Å2 / Biso min: 9.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.3 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.45→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 2 408 2367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212024
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.952782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87924.45883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73615307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.375158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021588
X-RAY DIFFRACTIONr_nbd_refined0.180.2992
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0790.2315
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.253
X-RAY DIFFRACTIONr_mcbond_it0.4981.51322
X-RAY DIFFRACTIONr_mcangle_it0.7922089
X-RAY DIFFRACTIONr_scbond_it1.6033820
X-RAY DIFFRACTIONr_scangle_it1.6754.5693
X-RAY DIFFRACTIONr_rigid_bond_restr1.46332142
X-RAY DIFFRACTIONr_sphericity_free1.3853410
X-RAY DIFFRACTIONr_sphericity_bonded1.04131957
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.548 162 -
Rwork0.423 2908 -
all-3070 -
obs--94.43 %

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