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- PDB-4kel: Atomic resolution crystal structure of Kallikrein-Related Peptida... -

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Basic information

Entry
Database: PDB / ID: 4kel
TitleAtomic resolution crystal structure of Kallikrein-Related Peptidase 4 complexed with a modified SFTI inhibitor FCQR(N)
Components
  • Kallikrein-4
  • Trypsin inhibitor 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Bowman-Birk Inhibitor / Protease / Protease Inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


biomineral tissue development / negative regulation of endopeptidase activity / amelogenesis / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / protein maturation / serine-type endopeptidase inhibitor activity ...biomineral tissue development / negative regulation of endopeptidase activity / amelogenesis / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / protein maturation / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine 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
Trypsin inhibitor 1 / Trypsin inhibitor 1 / Kallikrein-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.148 Å
AuthorsIlyichova, O.V. / Swedberg, J.E. / de Veer, S.J. / Sit, K.C. / Harris, J.M. / Buckle, A.M.
CitationJournal: Biochemistry / Year: 2019
Title: KLK4 Inhibition by Cyclic and Acyclic Peptides: Structural and Dynamical Insights into Standard-Mechanism Protease Inhibitors.
Authors: Riley, B.T. / Ilyichova, O. / de Veer, S.J. / Swedberg, J.E. / Wilson, E. / Hoke, D.E. / Harris, J.M. / Buckle, A.M.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 4, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kallikrein-4
B: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)25,5062
Polymers25,5062
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-10 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.844, 63.331, 41.191
Angle α, β, γ (deg.)90.00, 115.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kallikrein-4 / Enamel matrix serine proteinase 1 / Kallikrein-like protein 1 / KLK-L1 / Prostase / Serine protease 17


Mass: 23926.010 Da / Num. of mol.: 1 / Fragment: Related Peptidase 4, UNP residues 31-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4 / Plasmid: pET12a-proPSA-hK4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Trypsin inhibitor 1 / SFTI-1


Type: Cyclic peptide / Class: Trypsin inhibitor / Mass: 1579.863 Da / Num. of mol.: 1 / Mutation: modified FCQR(N) / Source method: obtained synthetically / Details: modified Sunflower Trypsin Inhibitor / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5, Trypsin inhibitor 1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE IS NATURAL VARIANT (VARIANT RS2569527)

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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: 1.84 Å3/Da / Density % sol: 33.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M lithium sulfate, 0.1M sodium acetate, 30% PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.148→63.37 Å / Num. all: 64890 / Num. obs: 64890 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 5.978 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.15-1.213.50.3694.393490.36998.1
3.64-63.375.90.05828.721280.05899.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BDG

2bdg


Resolution: 1.148→37.154 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.9255 / SU ML: 0.09 / σ(F): 1.36 / Phase error: 14.31 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1634 3300 5.09 %RANDOM
Rwork0.1366 ---
all0.1379 64855 --
obs0.1379 64855 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 39.72 Å2 / Biso mean: 12.4673 Å2 / Biso min: 4.1 Å2
Refinement stepCycle: LAST / Resolution: 1.148→37.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 0 209 1954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061938
X-RAY DIFFRACTIONf_angle_d1.1832650
X-RAY DIFFRACTIONf_chiral_restr0.083295
X-RAY DIFFRACTIONf_plane_restr0.006356
X-RAY DIFFRACTIONf_dihedral_angle_d12.285699
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1485-1.16490.18221330.14382465259894
1.1649-1.18220.15031340.13522514264897
1.1822-1.20070.1761210.13542572269399
1.2007-1.22040.18611360.13322516265298
1.2204-1.24150.19421300.13222574270499
1.2415-1.2640.15891320.12772509264198
1.264-1.28830.171240.12522590271498
1.2883-1.31460.17061380.12732529266799
1.3146-1.34320.16451400.11812563270399
1.3432-1.37450.18561230.11762592271599
1.3745-1.40890.14751500.116325242674100
1.4089-1.44690.16491380.11532567270599
1.4469-1.48950.14291210.11162596271799
1.4895-1.53760.13271370.10962577271499
1.5376-1.59260.15711330.10552592272599
1.5926-1.65630.12831400.10892555269599
1.6563-1.73170.14721420.11962567270999
1.7317-1.8230.1691530.127825682721100
1.823-1.93720.17681280.13182559268799
1.9372-2.08680.14881580.13552583274199
2.0868-2.29670.14661470.140825832730100
2.2967-2.6290.16521410.15725962737100
2.629-3.3120.18091630.167326192782100
3.312-37.17320.17331380.15112645278399

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