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- PDB-4k1e: Atomic resolution crystal structures of Kallikrein-Related Peptid... -

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Basic information

Entry
Database: PDB / ID: 4k1e
TitleAtomic resolution crystal structures of Kallikrein-Related Peptidase 4 complexed with a modified SFTI inhibitor FCQR
Components
  • Kallikrein-4KLK4
  • Trypsin inhibitor 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein-peptide complex / Bowman-Birk Inhibitor / Protease / Protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


biomineral tissue development / amelogenesis / negative regulation of endopeptidase activity / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / serine-type endopeptidase inhibitor activity / protease binding ...biomineral tissue development / amelogenesis / negative regulation of endopeptidase activity / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
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
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: 1.3 Å
AuthorsIlyichova, O.V. / Swedberg, J.E. / de Veer, S.J. / Sit, K.C. / Harris, J.M. / Buckle, A.M.
CitationJournal: Sci Rep / Year: 2016
Title: Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics
Authors: Riley, B.T. / Ilyichova, O. / Costa, M.G.S. / Porebski, B.T. / de Veer, S.J. / Swedberg, J.E. / Kass, I. / Harris, J.M. / Hoke, D.E. / Buckle, A.M.
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Other
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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-4
B: Trypsin inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6324
Polymers25,5072
Non-polymers1252
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-26 kcal/mol
Surface area9800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.780, 63.306, 41.181
Angle α, β, γ (deg.)90.00, 115.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kallikrein-4 / KLK4 / 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: pET12-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: PolypeptidePeptide / Class: Trypsin inhibitor / Mass: 1580.848 Da / Num. of mol.: 1 / Mutation: modified FCQR / Source method: obtained synthetically / Details: Modified Sunflower Trypsin Inhibitor / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5, Trypsin inhibitor 1
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
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: 1.83 Å3/Da / Density % sol: 32.88 %
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: Apr 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.12→37.12 Å / Num. obs: 70424 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 7.229 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.12-1.183.40.7262.110290199.6
3.54-37.123.40.0617.42134192.8

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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: 1.3→37.12 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.9152 / SU ML: 0.09 / σ(F): 1.36 / Phase error: 15.4 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1696 2305 5.12 %RANDOM
Rwork0.1396 ---
all0.1412 45043 --
obs0.1412 45043 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.4 Å2 / Biso mean: 13.144 Å2 / Biso min: 3.99 Å2
Refinement stepCycle: LAST / Resolution: 1.3→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 9 115 1860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081864
X-RAY DIFFRACTIONf_angle_d1.1592545
X-RAY DIFFRACTIONf_chiral_restr0.081285
X-RAY DIFFRACTIONf_plane_restr0.005337
X-RAY DIFFRACTIONf_dihedral_angle_d12.985667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.32830.1721190.127326972816100
1.3283-1.35920.18381400.126726512791100
1.3592-1.39320.18051530.126326752828100
1.3932-1.43080.17991290.126726922821100
1.4308-1.47290.17971320.120826992831100
1.4729-1.52050.15721460.111926432789100
1.5205-1.57480.1771440.114226642808100
1.5748-1.63790.14221530.115126662819100
1.6379-1.71240.18831180.118227332851100
1.7124-1.80270.17111640.120426532817100
1.8027-1.91570.16281470.125126652812100
1.9157-2.06360.16941610.128426662827100
2.0636-2.27120.15841520.138926832835100
2.2712-2.59980.17851490.156926822831100
2.5998-3.27510.18911620.173426902852100
3.2751-37.13480.15321360.15632579271594

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