[English] 日本語
Yorodumi
- PDB-4kga: Crystal structure of kallikrein-related peptidase 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kga
TitleCrystal structure of kallikrein-related peptidase 4
ComponentsKallikrein-4KLK4
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Kallikrein-4 / KLK4 / 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 / Nickel


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


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


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS NATURAL VARIANT (VARIANT RS2569527)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more