[English] 日本語
Yorodumi
- PDB-2bdi: Human Kallikrein 4 complex with cobalt and p-aminobenzamidine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bdi
TitleHuman Kallikrein 4 complex with cobalt and p-aminobenzamidine
ComponentsKallikrein-4KLK4
KeywordsHYDROLASE / serine proteinase / s1 subsite / 70-80 loop / Structural Proteomics in Europe / SPINE / Structural Genomics
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 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
: / P-AMINO BENZAMIDINE / Kallikrein-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDebela, M. / Bode, W. / Goettig, P. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site.
Authors: Debela, M. / Magdolen, V. / Grimminger, V. / Sommerhoff, C. / Messerschmidt, A. / Huber, R. / Friedrich, R. / Bode, W. / Goettig, P.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_conn.ptnr2_label_seq_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
C: Kallikrein-4
D: Kallikrein-4
E: Kallikrein-4
F: Kallikrein-4
G: Kallikrein-4
H: Kallikrein-4
I: Kallikrein-4
J: Kallikrein-4
K: Kallikrein-4
L: Kallikrein-4
M: Kallikrein-4
N: Kallikrein-4
O: Kallikrein-4
P: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,23136
Polymers382,81616
Non-polymers2,41520
Water8,215456
1
A: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1213
Polymers23,9261
Non-polymers1952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1213
Polymers23,9261
Non-polymers1952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1213
Polymers23,9261
Non-polymers1952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1213
Polymers23,9261
Non-polymers1952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: Kallikrein-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0622
Polymers23,9261
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.050, 73.860, 154.380
Angle α, β, γ (deg.)90.00, 102.41, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Kallikrein-4 / KLK4 / Prostase / Kallikrein-like protein 1 / KLK-L1 / Enamel matrix serine proteinase 1


Mass: 23926.010 Da / Num. of mol.: 16 / Fragment: Human Kallikrein 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, EMSP1, PRSS17, PSTS / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4]
References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-PBZ / P-AMINO BENZAMIDINE


Mass: 136.174 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C7H10N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.6 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 21, 2003 / Details: mirrors
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 95468 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.129 / Net I/σ(I): 6.99
Reflection shellResolution: 2.5→2.57 Å / % possible all: 76

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: hk4 with nickel

Resolution: 3→19.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1910575.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 3158 5 %RANDOM
Rwork0.258 ---
obs0.258 62929 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3653 Å2 / ksol: 0.318519 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-2.92 Å2
2---1.78 Å20 Å2
3---3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26720 0 164 456 27340
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.03
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.49
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.132
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.822.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 536 5.2 %
Rwork0.311 9779 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4PBZ.PARPBZ.TOP

+
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