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- PDB-5lpe: Kallikrein-related peptidase 10 complex with Zn2+ -

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Basic information

Entry
Database: PDB / ID: 5lpe
TitleKallikrein-related peptidase 10 complex with Zn2+
ComponentsKallikrein-10
KeywordsHYDROLASE / Serine protease / zymogen-like enzyme / Zn2+ inhibition / tumor suppressor
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / cell cycle / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine 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 ...Serine proteases, trypsin family, histidine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine 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 / molecular replacement / Resolution: 2.65 Å
AuthorsGoettig, P. / Debela, M. / Magdolen, V. / Bode, W. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP25003-B21 Austria
CitationJournal: Biol.Chem. / Year: 2016
Title: Structural basis for the Zn2+ inhibition of the zymogen-like kallikrein-related peptidase 10.
Authors: Debela, M. / Magdolen, V. / Bode, W. / Brandstetter, H. / Goettig, P.
History
DepositionAug 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_remark / pdbx_data_processing_status ...database_PDB_remark / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _database_PDB_remark.text
Revision 1.4Jan 10, 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-10
B: Kallikrein-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,16410
Polymers51,4572
Non-polymers7078
Water2,234124
1
A: Kallikrein-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0825
Polymers25,7291
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0825
Polymers25,7291
Non-polymers3544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.914, 67.037, 57.768
Angle α, β, γ (deg.)90.000, 104.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kallikrein-10 / / Normal epithelial cell-specific 1 / Protease serine-like 1


Mass: 25728.527 Da / Num. of mol.: 2 / Fragment: UNP residues 43-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK10, NES1, PRSSL1 / Production host: Escherichia coli (E. coli)
References: UniProt: O43240, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.93 Å3/Da / Density % sol: 36.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 100 mM ammonium sulphate, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 26, 2004 / Details: quartz mirror
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.65→55.96 Å / Num. obs: 11339 / % possible obs: 98.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 41.08 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.104 / Net I/av σ(I): 5.938 / Net I/σ(I): 8.1
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 0.975 / CC1/2: 0.715 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å41.01 Å
Translation2.8 Å41.01 Å

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Processing

Software
NameVersionClassification
AUTOMARdata collection
MOSFLMdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BDG

2bdg


Resolution: 2.65→43.565 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.72
RfactorNum. reflection% reflection
Rfree0.2777 593 5.24 %
Rwork0.2198 --
obs0.2229 11317 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.91 Å2 / Biso mean: 37.4763 Å2 / Biso min: 13.04 Å2
Refinement stepCycle: final / Resolution: 2.65→43.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 32 124 3275
Biso mean--52.77 36.79 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113234
X-RAY DIFFRACTIONf_angle_d1.4334403
X-RAY DIFFRACTIONf_chiral_restr0.065479
X-RAY DIFFRACTIONf_plane_restr0.008561
X-RAY DIFFRACTIONf_dihedral_angle_d24.7311196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6502-2.74490.3838520.280910741126100
2.7449-2.85480.2964570.266110831140100
2.8548-2.98470.3004710.24971048111999
2.9847-3.1420.3085590.244110841143100
3.142-3.33880.2856660.22341065113199
3.3388-3.59650.2947800.21531065114599
3.5965-3.95820.2592570.20871081113899
3.9582-4.53040.2624520.19211078113098
4.5304-5.70580.2421460.18951084113097
5.7058-43.5710.2538530.23481062111594

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