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- PDB-3gyl: Structure of Prostasin at 1.3 Angstroms resolution in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3gyl
TitleStructure of Prostasin at 1.3 Angstroms resolution in complex with a Calcium Ion.
ComponentsProstasinPRSS8
KeywordsHYDROLASE / PROSTASIN / ENAC / ZYMOGEN / DIVALENT CATION / CHANNEL ACTIVATING / Cell membrane / Disulfide bond / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Transmembrane
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 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
DepositionApr 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)28,4514
Polymers28,2271
Non-polymers2243
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.112, 54.039, 82.553
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 / PRSS8 / Serine protease 8 / Prostasin light chain / Prostasin heavy chain


Mass: 28226.553 Da / Num. of mol.: 1
Fragment: UNP residues 45-305, Peptidase S1 Domain of Prostasin heavy chain
Mutation: C122S,N127Q,C170S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCAP1, PRSS8 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9
References: UniProt: Q16651, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% Peg-3000, 0.2M Calcium Acetate buffered with 0.1M Tris at pH 7.0,, 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 315 / Detector: CCD / Date: Feb 24, 2004 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→45 Å / Num. obs: 57859 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 6.52 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 18.9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5058 / Rsym value: 0.763 / % possible all: 84.5

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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 SYNTHESIS
Starting model: PDB ENTRY 3E1X

3e1x


Resolution: 1.3→45 Å / SU ML: 1.04 / Isotropic thermal model: anisotropic / Cross valid method: througout / σ(F): 0.12 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1776 2630 4.94 %RANDOM
Rwork0.1531 ---
obs0.1544 53269 88.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.487 Å2 / ksol: 0.437 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0451 Å20 Å20 Å2
2--1.8413 Å20 Å2
3----1.7963 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 13 367 2253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.017
X-RAY DIFFRACTIONf_angle_deg1.86
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32370.2868940.25792042X-RAY DIFFRACTION68
1.3237-1.34910.27761080.22212069X-RAY DIFFRACTION70
1.3491-1.37670.21271070.20852222X-RAY DIFFRACTION75
1.3767-1.40660.18731290.20052250X-RAY DIFFRACTION76
1.4066-1.43930.21341050.18532360X-RAY DIFFRACTION79
1.4393-1.47530.22171340.17132567X-RAY DIFFRACTION85
1.4753-1.51520.18281150.15862556X-RAY DIFFRACTION86
1.5152-1.55980.19241410.14652612X-RAY DIFFRACTION88
1.5598-1.61020.15521420.1362696X-RAY DIFFRACTION90
1.6102-1.66770.17011340.13722742X-RAY DIFFRACTION91
1.6677-1.73450.17491340.14572793X-RAY DIFFRACTION93
1.7345-1.81340.18091740.1342798X-RAY DIFFRACTION94
1.8134-1.9090.18241360.13812875X-RAY DIFFRACTION96
1.909-2.02860.15781760.13282907X-RAY DIFFRACTION97
2.0286-2.18530.14511570.13492977X-RAY DIFFRACTION98
2.1853-2.40520.17681700.14112955X-RAY DIFFRACTION98
2.4052-2.75320.18511580.15013028X-RAY DIFFRACTION99
2.7532-3.46850.1531510.13933052X-RAY DIFFRACTION99
3.4685-45.28360.15981650.15123138X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 14.4561 Å / Origin y: -0.0525 Å / Origin z: -15.8634 Å
111213212223313233
T0.0178 Å20.0011 Å20.0024 Å2-0.0166 Å2-0 Å2--0.0304 Å2
L0.1612 °2-0.0577 °20.0425 °2-0.2948 °2-0.0404 °2--0.4589 °2
S-0.0066 Å °-0.0046 Å °-0.0084 Å °0.0026 Å °-0.0011 Å °0.0267 Å °-0.0099 Å °-0.0317 Å °0.0069 Å °
Refinement TLS groupSelection details: chain B

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