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- PDB-7jqk: Crystal structure of the R64A mutant of Bauhinia Bauhinioides Kal... -

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Basic information

Entry
Database: PDB / ID: 7jqk
TitleCrystal structure of the R64A mutant of Bauhinia Bauhinioides Kallikrein Inhibitor complexed with Human Kallikrein 4
Components
  • Kallikrein-4
  • Kunitz-type inihibitor
KeywordsSTRUCTURAL PROTEIN / HYDROLASE/INHIBITOR / Human Kallikrein 4 / Bauhinia Bauhiniordes Kallikrein Inhibitor / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


biomineral tissue development / 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 activity / proteolysis ...biomineral tissue development / 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 activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / 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. ...Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / Kunitz-type inihibitor / Kallikrein-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Bauhinia bauhinioides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.33 Å
AuthorsLi, M. / Wlodawer, A. / Gustchina, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI.
Authors: Li, M. / Srp, J. / Mares, M. / Wlodawer, A. / Gustchina, A.
History
DepositionAug 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
E: Kallikrein-4
I: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0648
Polymers41,9392
Non-polymers1,1256
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-43 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.036, 104.036, 86.801
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11E-534-

HOH

21E-737-

HOH

31E-772-

HOH

41I-513-

HOH

51I-556-

HOH

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Components

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Protein , 2 types, 2 molecules EI

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


Mass: 23942.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, EMSP1, PRSS17, PSTS / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Kunitz-type inihibitor


Mass: 17997.352 Da / Num. of mol.: 1 / Mutation: R64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bauhinia bauhinioides (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VEQ7

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Non-polymers , 4 types, 650 molecules

#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0M Ammonium Sulfate 2% PEG400, 10mM CdCl2 at pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→90.1 Å / Num. obs: 119509 / % possible obs: 95.4 % / Redundancy: 8.8 % / Rsym value: 0.052 / Net I/σ(I): 24
Reflection shellResolution: 1.33→1.35 Å / Num. unique obs: 3446 / Rsym value: 0.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.33→90.1 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1533 3684 3.1 %RANDOM
Rwork0.1189 ---
obs0.1199 115784 95.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 170.4 Å2 / Biso mean: 31.0275 Å2 / Biso min: 12.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å2-0 Å2
2---0.05 Å20 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 1.33→90.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 9 645 3596
Biso mean--53.44 49.43 -
Num. residues----389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0123162
X-RAY DIFFRACTIONr_angle_refined_deg2.3141.6284320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0095419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99424.207145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97515524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8491511
X-RAY DIFFRACTIONr_chiral_restr0.150.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022424
X-RAY DIFFRACTIONr_rigid_bond_restr10.62233162
LS refinement shellResolution: 1.33→1.361 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.289 198 -
Rwork0.289 5733 -
obs--64.66 %

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