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- PDB-2qxi: High resolution structure of Human Kallikrein 7 in Complex with S... -

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Basic information

Entry
Database: PDB / ID: 2qxi
TitleHigh resolution structure of Human Kallikrein 7 in Complex with Suc-Ala-Ala-Pro-Phe-chloromethylketone
ComponentsKallikrein-7
KeywordsHYDROLASE / S1 pocket / chloromethyl ketone / alternate conformations / Alternative splicing / Glycoprotein / Protease / Secreted / Serine protease / Zymogen
Function / homology
Function and homology information


stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / extracellular matrix disassembly / epidermis development / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / metalloendopeptidase activity ...stratum corneum chymotryptic enzyme / positive regulation of antibacterial peptide production / epidermal lamellar body / cornified envelope / extracellular matrix disassembly / epidermis development / Degradation of the extracellular matrix / serine-type peptidase activity / secretory granule / metalloendopeptidase activity / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region
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
Chem-K7J / Kallikrein-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 Å
AuthorsDebela, M. / Hess, P. / Magdolen, V. / Schechter, N.M. / Bode, W. / Goettig, P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Chymotryptic specificity determinants in the 1.0 A structure of the zinc-inhibited human tissue kallikrein 7.
Authors: Debela, M. / Hess, P. / Magdolen, V. / Schechter, N.M. / Steiner, T. / Huber, R. / Bode, W. / Goettig, P.
History
DepositionAug 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_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

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Assembly

Deposited unit
A: Kallikrein-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0202
Polymers24,4811
Non-polymers5391
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.254, 56.953, 45.533
Angle α, β, γ (deg.)90.000, 101.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kallikrein-7 / hK7 / Stratum corneum chymotryptic enzyme / hSCCE / Serine protease 6


Mass: 24481.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK7, PRSS6, SCCE / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P49862, stratum corneum chymotryptic enzyme
#2: Chemical ChemComp-K7J / N-(3-carboxypropanoyl)-L-alanyl-L-alanyl-N-[(2S,3S)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]-L-prolinamide / SUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE


Mass: 539.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35ClN4O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% MPD, 0.1 M sodium cacodylate, 0.2 M magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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 30, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 0.999→44.64 Å / Num. all: 97071 / Num. obs: 97071 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 9.7
Reflection shellResolution: 1→1.05 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.4 / Num. measured all: 38559 / Num. unique all: 13473 / Rsym value: 0.28 / % possible all: 89.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
SHELXrefinement
PDB_EXTRACT3data extraction
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LO6

1lo6


Resolution: 1→10 Å / Num. parameters: 18790 / Num. restraintsaints: 23566 / Cross valid method: FREE R / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF), riding hydrogen model of SHELX was employed in the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.159 4932 5.4 %RANDOM
Rwork0.131 ---
all0.141 97066 --
obs-97066 89.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 16.863 Å2
Refine analyzeLuzzati coordinate error obs: 0.089 Å
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 45 225 2089
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.336
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.077
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.078
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1→1.1 Å /
RfactorNum. reflection
Rwork0.227 -
obs-21862

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