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- PDB-5lpf: Kallikrein-related peptidase 10 -

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Basic information

Entry
Database: PDB / ID: 5lpf
TitleKallikrein-related peptidase 10
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 / secretory granule / protein maturation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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: 2.7 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: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallikrein-10
B: Kallikrein-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1299
Polymers51,4572
Non-polymers6727
Water2,432135
1
A: Kallikrein-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1135
Polymers25,7291
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0174
Polymers25,7291
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.602, 66.841, 57.900
Angle α, β, γ (deg.)90.000, 104.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 21:23 or resseq 25:33 or (resid...
21(chain B and (resseq 21:23 or resseq 25:33 or (resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALA(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA21 - 239 - 11
12GLYGLYLEULEU(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA25 - 3313 - 21
13PHEPHEPHEPHE(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA3422
14PROPROASNASN(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA21 - 2459 - 234
15PROPROASNASN(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA21 - 2459 - 234
16PROPROASNASN(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA21 - 2459 - 234
17PROPROASNASN(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA21 - 2459 - 234
18PROPROASNASN(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA21 - 2459 - 234
19PROPROASNASN(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA21 - 2459 - 234
110PROPROASNASN(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA21 - 2459 - 234
111PROPROASNASN(chain A and (resseq 21:23 or resseq 25:33 or (resid...AA21 - 2459 - 234
21PROPROALAALA(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB21 - 239 - 11
22GLYGLYLEULEU(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB25 - 3313 - 21
23PHEPHEPHEPHE(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB3422
24SERSERASNASN(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB20 - 2458 - 234
25SERSERASNASN(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB20 - 2458 - 234
26SERSERASNASN(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB20 - 2458 - 234
27SERSERASNASN(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB20 - 2458 - 234
28SERSERASNASN(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB20 - 2458 - 234
29SERSERASNASN(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB20 - 2458 - 234
210SERSERASNASN(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB20 - 2458 - 234
211SERSERASNASN(chain B and (resseq 21:23 or resseq 25:33 or (resid...BB20 - 2458 - 234

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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


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.95 Å3/Da / Density % sol: 37.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1 M ammonium sulphate, 0.1 M 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: 2.7→51.94 Å / Num. obs: 10481 / % possible obs: 95 % / Redundancy: 3.3 % / Biso Wilson estimate: 35.81 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.065 / Net I/av σ(I): 10.132 / Net I/σ(I): 14.4
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.989 / CC1/2: 0.947 / % possible all: 93.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å41.01 Å
Translation2.7 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: 2.7→36.694 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.1
RfactorNum. reflection% reflection
Rfree0.2849 588 5.65 %
Rwork0.2234 --
obs0.2268 10400 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.67 Å2 / Biso mean: 31.2862 Å2 / Biso min: 7.51 Å2
Refinement stepCycle: final / Resolution: 2.7→36.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 35 135 3277
Biso mean--61.07 26.79 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113221
X-RAY DIFFRACTIONf_angle_d1.1284392
X-RAY DIFFRACTIONf_chiral_restr0.06478
X-RAY DIFFRACTIONf_plane_restr0.007559
X-RAY DIFFRACTIONf_dihedral_angle_d24.6191189
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1486X-RAY DIFFRACTION17.052TORSIONAL
12B1486X-RAY DIFFRACTION17.052TORSIONAL
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 (%)
2.7001-2.79660.3523610.281992198291
2.7966-2.90850.3947630.288210491112100
2.9085-3.04080.3723740.274810171091100
3.0408-3.2010.3101650.242410261091100
3.201-3.40150.3113480.231510561104100
3.4015-3.66390.291460.234878382980
3.6639-4.03220.3452440.232281485885
4.0322-4.61470.2025720.169910271099100
4.6147-5.81030.2514490.189110711120100
5.8103-36.69690.2354660.2211048111499

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