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- PDB-1lo6: Human Kallikrein 6 (hK6) active form with benzamidine inhibitor a... -

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Basic information

Entry
Database: PDB / ID: 1lo6
TitleHuman Kallikrein 6 (hK6) active form with benzamidine inhibitor at 1.56 A resolution
ComponentsKallikrein 6
KeywordsHYDROLASE / serine protease / kallikrein / human kallikrein 6 / hk6 / benzamidine / protease / brain serine protease / myelencephalon specific protease / MSP / zyme / protease M / neurosin
Function / homology
Function and homology information


tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / amyloid precursor protein metabolic process / hormone metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...tissue regeneration / positive regulation of G protein-coupled receptor signaling pathway / cornified envelope / amyloid precursor protein metabolic process / hormone metabolic process / intercellular bridge / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / collagen catabolic process / myelination / secretory granule / central nervous system development / response to wounding / nuclear membrane / serine-type endopeptidase activity / nucleolus / endoplasmic reticulum / mitochondrion / extracellular space / extracellular region / nucleoplasm / 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
BENZAMIDINE / Kallikrein-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBernett, M.J. / Blaber, S.I. / Scarisbrick, I.A. / Dhanarajan, P. / Thompson, S.M. / Blaber, M.
CitationJournal: To be Published
Title: Crystal structure and biochemical characterization of human kallikrein 6 reveals a trypsin-like kallikrein is expressed in the central nervous system
Authors: Bernett, M.J. / Blaber, S.I. / Scarisbrick, I.A. / Dhanarajan, P. / Thompson, S.M. / Blaber, M.
History
DepositionMay 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallikrein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6773
Polymers24,5331
Non-polymers1442
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.207, 61.814, 85.838
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 Kallikrein 6 / / HK6


Mass: 24532.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pBAC3 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92876
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (W/V) PEG 4000, 0.2M Magnesium chloride hexahydrate, 0.1M Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONAPS 14-BM-C20.9
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEOct 24, 2001OSMIC BLUE CONFOCAL MIRRORS
ADSC QUANTUM 42CCDApr 14, 2002
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.91
ReflectionResolution: 1.56→25.97 Å / Num. all: 30440 / Num. obs: 28869 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 37.5
Reflection shellResolution: 1.56→1.6 Å / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 4.3 / % possible all: 89.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L2E

1l2e


Resolution: 1.56→25.97 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.223 753 RANDOM
Rwork0.196 --
all0.229 30440 -
obs0.197 26163 -
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 1.56→25.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 10 141 1864
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006549
X-RAY DIFFRACTIONc_angle_deg1.51654
LS refinement shellResolution: 1.56→1.66 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection
Rfree0.234 89
Rwork0.222 -
obs-3068

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