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- PDB-4k8y: Atomic resolution crystal structures of Kallikrein-Related Peptid... -

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Basic information

Entry
Database: PDB / ID: 4k8y
TitleAtomic resolution crystal structures of Kallikrein-Related Peptidase 4 complexed with Sunflower Trypsin Inhibitor (SFTI-1)
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 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 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,4622
Polymers25,4622
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-9 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.927, 75.747, 39.743
Angle α, β, γ (deg.)90.00, 95.73, 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)pLysS
References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide Trypsin inhibitor 1 / SFTI-1


Type: Polypeptide / Class: Trypsin inhibitor / Mass: 1535.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This inhibitor occurs naturally in sunflowers / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5, Trypsin inhibitor 1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 1.88 Å3/Da / Density % sol: 34.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.2M Lithium Sulfate, 0.1M Sodium Acetate, 20%(w/v) PEG 8000, pH 4.8, 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: 0.8266 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2012
RadiationMonochromator: Si(111): 4.5-21 keV, Si(311): 11-35 keV / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1→29.3 Å / Num. all: 100687 / Num. obs: 100687 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 6.029 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.9 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1-1.050.4352.7147100.43584.9
3.16-29.30.08316.331590.08392.6

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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→29.296 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.9167 / SU ML: 0.09 / σ(F): 1.34 / Phase error: 15.56 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1702 5026 4.99 %RANDOM
Rwork0.15 ---
obs0.1511 100641 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 40.02 Å2 / Biso mean: 11.9559 Å2 / Biso min: 4.28 Å2
Refinement stepCycle: LAST / Resolution: 1→29.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 0 326 2072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061991
X-RAY DIFFRACTIONf_angle_d1.2122730
X-RAY DIFFRACTIONf_chiral_restr0.083305
X-RAY DIFFRACTIONf_plane_restr0.006369
X-RAY DIFFRACTIONf_dihedral_angle_d13.159734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 36

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1-1.00940.27421510.250726682819100
1.0094-1.01920.21761320.23752641277399
1.0192-1.02940.21541390.22222670280999
1.0294-1.040.22971140.20912627274199
1.04-1.05110.23031420.195326492791100
1.0511-1.06270.2341490.18552646279599
1.0627-1.07470.17091430.1726572800100
1.0747-1.08740.18951420.16252628277099
1.0874-1.10060.20971400.15972699283999
1.1006-1.11460.14871010.150126122713100
1.1146-1.12920.17841430.148826582801100
1.1292-1.14470.1761330.14752666279999
1.1447-1.16110.17121440.144926502794100
1.1611-1.17840.17621550.146926322787100
1.1784-1.19680.1561620.1462606276899
1.1968-1.21640.16781610.14832643280499
1.2164-1.23740.17941440.14362660280499
1.2374-1.25990.17521280.14432629275799
1.2599-1.28410.18711380.139526902828100
1.2841-1.31040.16791380.1392615275399
1.3104-1.33880.1341270.131526922819100
1.3388-1.370.16161320.13662648278099
1.37-1.40430.16541340.134826622796100
1.4043-1.44220.16671450.13422634277999
1.4422-1.48470.14371270.12962647277499
1.4847-1.53260.14211470.129326912838100
1.5326-1.58730.15271650.130326332798100
1.5873-1.65090.15481510.13326582809100
1.6509-1.7260.17521300.138826832813100
1.726-1.8170.16321500.143526522802100
1.817-1.93080.16321340.143326782812100
1.9308-2.07990.15651230.145127012824100
2.0799-2.28910.18181360.150226922828100
2.2891-2.62020.16971380.159326812819100
2.6202-3.30040.18461410.16427102851100
3.3004-29.30830.15531470.14612607275496

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