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- PDB-6o21: Crystal Structure of Human KLK4 in Complex With Cleaved SFTI-FCQR... -

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Basic information

Entry
Database: PDB / ID: 6o21
TitleCrystal Structure of Human KLK4 in Complex With Cleaved SFTI-FCQR(Asn14)[1,14] Inhibitor
Components
  • Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a
  • Trypsin inhibitor 1
KeywordsHYDROLASE/HYDROLASE Inhibitor / Kallikrein-related peptidase 4 / KLK4 / Sunflower Trypsin Inhibitor / SFTI / Laskowski mechanism inhibitor / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


biomineral tissue development / amelogenesis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / protein catabolic process / serine-type endopeptidase activity / proteolysis / extracellular space ...biomineral tissue development / amelogenesis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / protein catabolic process / 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 / 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 / Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a / Kallikrein-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsIlyichova, O.V. / 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
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / pdbx_molecule_features / struct / struct_keywords
Item: _entity.pdbx_description / _struct.pdbx_descriptor ..._entity.pdbx_description / _struct.pdbx_descriptor / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a
B: Trypsin inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9126
Polymers25,5062
Non-polymers4064
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-55 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.529, 63.145, 40.893
Angle α, β, γ (deg.)90.000, 114.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a / Kallikrein B1 / Kallikrein-4


Mass: 23926.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, KLNB1, hCG_1641510 / Plasmid: pET12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C4DFQ5, UniProt: Q9Y5K2*PLUS
#2: Protein/peptide Trypsin inhibitor 1 / acyclic SFTI-FCQR(Asn14)


Type: Cyclic peptide / Class: Trypsin inhibitor / Mass: 1579.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: Trypsin inhibitor 1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.86 Å3/Da / Density % sol: 34.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30 % (w/v) PEG 8000, 0.1 M sodium acetate, 0.2 M lithium sulfate, pH 4.5
PH range: 4.5-4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.15→63.15 Å / Num. obs: 62317 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.031 / Rrim(I) all: 0.068 / Net I/σ(I): 13
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.368 / Num. unique obs: 3008 / CC1/2: 0.883 / Rpim(I) all: 0.227 / Rrim(I) all: 0.434 / % possible all: 93.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.15 Å37.09 Å
Translation1.15 Å37.09 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KEL

4kel


Resolution: 1.15→37.085 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.22
RfactorNum. reflection% reflection
Rfree0.1634 3283 5.27 %
Rwork0.1297 --
obs0.1315 62287 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.23 Å2 / Biso mean: 12.8976 Å2 / Biso min: 3.9 Å2
Refinement stepCycle: final / Resolution: 1.15→37.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 37 238 1981
Biso mean--26.53 23.51 -
Num. residues----231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.16720.23111330.18842505263893
1.1672-1.18540.22671530.16192430258394
1.1854-1.20490.19481800.16062499267994
1.2049-1.22560.21651530.15812458261195
1.2256-1.24790.20281420.15112500264295
1.2479-1.27190.15481350.14152551268695
1.2719-1.29790.16951180.13672520263895
1.2979-1.32610.16821170.13352560267795
1.3261-1.3570.16621240.12352571269595
1.357-1.39090.15171300.12332527265796
1.3909-1.42850.14911260.12222584271096
1.4285-1.47050.16441470.11762574272196
1.4705-1.5180.14351410.11272559270097
1.518-1.57230.15211570.11252563272097
1.5723-1.63520.1511420.10982571271397
1.6352-1.70960.17481390.1172591273097
1.7096-1.79980.1361670.11932570273798
1.7998-1.91250.1511340.1192626276098
1.9125-2.06020.14161340.12022633276798
2.0602-2.26750.14051300.11742637276799
2.2675-2.59550.15341770.12952606278399
2.5955-3.26980.16311510.13912661281299
3.2698-37.10460.18251530.1392708286199

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