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- PDB-4kga: Crystal structure of kallikrein-related peptidase 4 -

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Basic information

Entry
Database: PDB / ID: 4kga
TitleCrystal structure of kallikrein-related peptidase 4
ComponentsKallikrein-4
KeywordsHYDROLASE / KLK4 / Kallikrein-4 / Serine protease / Protease
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 maturation / 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 maturation / 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
NICKEL (II) ION / Kallikrein-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2118
Polymers47,8522
Non-polymers3596
Water1,00956
1
A: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1054
Polymers23,9261
Non-polymers1793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1054
Polymers23,9261
Non-polymers1793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.308, 99.308, 41.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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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.: 2 / 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)
References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10mM NiCl2, 100mM Tris, 20% PEG2000 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95368 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95368 Å / Relative weight: 1
ReflectionResolution: 2.32→70.22 Å / Num. all: 17693 / Num. obs: 17693 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 43.593 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.32-2.455.80.7912.125390.791100
7.34-70.226.30.04836.56100.04899.9

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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: 2.32→49.654 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.7365 / SU ML: 0.3 / σ(F): 1.95 / Phase error: 32.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 898 5.08 %RANDOM
Rwork0.2198 ---
all0.2222 17689 --
obs0.2222 17689 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.6 Å2 / Biso mean: 65.89 Å2 / Biso min: 29.39 Å2
Refinement stepCycle: LAST / Resolution: 2.32→49.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 12 56 3264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033307
X-RAY DIFFRACTIONf_angle_d0.9054498
X-RAY DIFFRACTIONf_chiral_restr0.034516
X-RAY DIFFRACTIONf_plane_restr0.004585
X-RAY DIFFRACTIONf_dihedral_angle_d13.0271145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3202-2.46550.40611680.345427542922
2.4655-2.65590.33891340.306727692903
2.6559-2.92310.34611400.283228052945
2.9231-3.3460.31521540.254927542908
3.346-4.21530.23941540.183328012955
4.2153-49.66520.19791480.174629083056
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)
14.27480.621.45793.84241.722.8047-0.3354-1.344-0.03791.40410.23870.6038-0.2028-0.32170.18060.52110.1318-0.1390.53520.05140.171620.9342-40.313916.4876
20.48420.2022-0.14632.66791.75932.39830.0954-0.967-0.36670.1530.1122-0.3895-0.2631-0.4017-0.05260.62090.1533-0.15180.87210.01820.398715.7173-40.16521.1653
33.2077-0.27440.27132.4107-0.74041.7821-0.2885-0.29180.58320.24590.0395-0.0544-0.0132-0.18360.23470.46290.0432-0.15610.4669-0.04240.26824.9737-38.069610.3919
45.2805-0.868-0.65482.62460.81441.6152-0.0692-0.32690.08590.1967-0.0927-0.2936-0.16410.32590.03740.32390.0029-0.11810.29770.05980.386234.0769-39.00284.6776
54.62140.6231-1.43333.42080.18282.39330.46140.5634-0.14960.017-0.2466-0.02620.03080.14980.1120.29510.0306-0.09630.18170.01140.295626.5557-41.69733.3632
62.34821.0880.0525.8619-0.06471.8526-0.44170.8823-0.7619-1.44170.1474-0.60990.06220.13780.27150.538-0.03440.10180.4467-0.11550.6052-4.9943-30.11-8.7912
70.4676-1.3552-1.0317.85053.69032.30620.20630.6407-0.1012-1.4809-0.40370.0505-0.4543-0.48730.05740.68290.0788-0.0940.5859-0.09970.6469-10.8736-30.9064-12.5937
83.64540.92240.31815.71330.70651.3545-0.09360.4444-0.4666-0.3799-0.0266-0.09380.092-0.01490.14310.2505-0.0090.06760.26010.01290.4053-5.7895-27.4611-2.8285
93.34550.95690.95375.39261.44361.23450.01260.001-0.18440.2359-0.2431-0.1533-0.10840.08790.16740.33570.00760.02670.29870.08120.3526-2.1939-20.63913.8379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 17:67)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 68:90)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 91:160)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 161:209)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 210:239)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 17:54)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 55:81)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 82:160)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 161:239)

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