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- PDB-5ms3: Kallikrein-related peptidase 8 calcium complex -

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Basic information

Entry
Database: PDB / ID: 5ms3
TitleKallikrein-related peptidase 8 calcium complex
ComponentsKallikrein-8
KeywordsHYDROLASE / trypsin-like serine protease / Ca2+ complex / free active site / synaptic remodeling
Function / homology
Function and homology information


kallikrein 8 / Formation of the cornified envelope / regulation of synapse organization / keratinocyte proliferation / serine protease inhibitor complex / neuron projection morphogenesis / memory / response to wounding / serine-type endopeptidase activity / proteolysis ...kallikrein 8 / Formation of the cornified envelope / regulation of synapse organization / keratinocyte proliferation / serine protease inhibitor complex / neuron projection morphogenesis / memory / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytoplasm
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsDebela, M. / Magdolen, V. / Skala, W. / Bode, W. / Brandstetter, H. / Goettig, P.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP25003-B21 Austria
CitationJournal: To Be Published
Title: Specificity profiles and antagonistic Ca2+ and Zn2+ regulation of human KLK8/neuropsin activity by modules identified in crystal structures
Authors: Debela, M. / Magdolen, V. / Skala, W. / Craik, C.S. / Schneider, E.L. / Biniossek, M.L. / Schilling, O. / Elsaesser, B. / Bode, W. / Brandstetter, H. / Goettig, P.
History
DepositionDec 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kallikrein-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5252
Polymers24,4851
Non-polymers401
Water1,51384
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.997, 51.741, 82.863
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 Kallikrein-8 / hK8 / Neuropsin / NP / Ovasin / Serine protease 19 / Serine protease TADG-14 / Tumor-associated ...hK8 / Neuropsin / NP / Ovasin / Serine protease 19 / Serine protease TADG-14 / Tumor-associated differentially expressed gene 14 protein


Mass: 24484.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK8, NRPN, PRSS19, TADG14, UNQ283/PRO322 / Production host: Escherichia coli (E. coli) / References: UniProt: O60259, kallikrein 8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 38.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 35% (v/v) tert-Butanol, 0.1 M tri-Na citrate/citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97469 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2008 / Details: Mirrors
RadiationMonochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97469 Å / Relative weight: 1
ReflectionResolution: 2.3→82.86 Å / Num. obs: 9263 / % possible obs: 99.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 21.26 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.158 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.3-2.386.60.4030.966197.3
8.9-82.869.20.0760.996199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å43.89 Å
Translation2.3 Å43.89 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.27data scaling
PHASER2.6.1phasing
PHENIX1.10.1-2155refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NPM

1npm


Resolution: 2.3→43.888 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 28.78
RfactorNum. reflection% reflection
Rfree0.2656 435 4.73 %
Rwork0.2213 --
obs0.2234 9190 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.75 Å2 / Biso mean: 29.3418 Å2 / Biso min: 11.56 Å2
Refinement stepCycle: final / Resolution: 2.3→43.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 1 84 1796
Biso mean--26.19 28.99 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061764
X-RAY DIFFRACTIONf_angle_d0.7212392
X-RAY DIFFRACTIONf_chiral_restr0.048255
X-RAY DIFFRACTIONf_plane_restr0.006317
X-RAY DIFFRACTIONf_dihedral_angle_d12.4091064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.38230.332440.299882887298
2.3823-2.47770.3504460.2752852898100
2.4777-2.59050.3236480.2734853901100
2.5905-2.7270.2956360.2493870906100
2.727-2.89790.2854430.254186690999
2.8979-3.12150.2685350.2434869904100
3.1215-3.43560.3315400.2089886926100
3.4356-3.93240.2887400.1926892932100
3.9324-4.95340.1722430.1686894937100
4.9534-43.89580.2281600.21239451005100

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