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- PDB-7jow: Crystal structure of BbKI complexed with Human Kallikrein 4 -

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Basic information

Entry
Database: PDB / ID: 7jow
TitleCrystal structure of BbKI complexed with Human Kallikrein 4
Components
  • Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a
  • Kunitz-type inihibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / PLANT PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


amelogenesis / endopeptidase inhibitor activity / extracellular matrix disassembly / protein catabolic process / serine-type endopeptidase activity / proteolysis
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. ...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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / UREA / Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a / Kunitz-type inihibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
Bauhinia bauhinioides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsLi, M. / Wlodawer, A. / Gustchina, A.
CitationJournal: Acta Crystallogr.,Sect.D / 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 7, 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.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.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Kallikrein 4 (Prostase, enamel matrix, prostate), isoform CRA_a
I: Kunitz-type inihibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4456
Polymers41,8222
Non-polymers6224
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-22 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.495, 100.495, 167.298
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11I-992-

HOH

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Components

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Protein , 2 types, 2 molecules EI

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C4DFQ5
#2: Protein Kunitz-type inihibitor


Mass: 17896.316 Da / Num. of mol.: 1
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 , 5 types, 219 molecules

#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-URE / UREA / Urea


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.4M Ammounium Sulfate, 2% PEG400 10mM CdCl2

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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: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50.01 Å / Num. obs: 39402 / % possible obs: 100 % / Redundancy: 16.8 % / Rsym value: 0.076 / Net I/σ(I): 43.34
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 1.83 / Num. unique obs: 1906 / Rsym value: 1.204 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JOD

7jod


Resolution: 1.91→50.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.086 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1081 3.1 %RANDOM
Rwork0.1743 ---
obs0.1753 33971 88.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.74 Å2 / Biso mean: 25.633 Å2 / Biso min: 11.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.17 Å2-0 Å2
2---0.33 Å2-0 Å2
3---1.08 Å2
Refinement stepCycle: final / Resolution: 1.91→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 14 215 3163
Biso mean--42.68 34.34 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0133065
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172786
X-RAY DIFFRACTIONr_angle_refined_deg2.2761.6324179
X-RAY DIFFRACTIONr_angle_other_deg1.5561.5716517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg22.1065.697416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65123.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67215481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5981511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02618
LS refinement shellResolution: 1.91→1.955 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.317 33 -
Rwork0.226 1055 -
obs--37.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0683-0.4294-0.58871.65760.84211.6252-0.00130.02710.0952-0.1818-0.12050.0425-0.1228-0.2280.12180.32980.0714-0.07180.0589-0.01370.072224.81616.058913.3115
22.3994-0.76440.62210.5581-0.00132.0309-0.10540.10710.18060.0478-0.0132-0.08490.18850.25190.11860.32270.0888-0.02770.06820.04460.079452.77464.153415.5093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E16 - 244
2X-RAY DIFFRACTION2I1 - 163

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