[English] 日本語
Yorodumi
- PDB-1gvl: Human prokallikrein 6 (hK6)/ prozyme/ proprotease M/ proneurosin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gvl
TitleHuman prokallikrein 6 (hK6)/ prozyme/ proprotease M/ proneurosin
ComponentsKALLIKREIN 6
KeywordsHYDROLASE / ZYMOGEN / HUMAN KALLIKREIN
Function / homology
Function and homology information


tissue regeneration / cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / hormone metabolic process / amyloid precursor protein metabolic process / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...tissue regeneration / cornified envelope / positive regulation of G protein-coupled receptor signaling pathway / hormone metabolic process / amyloid precursor protein metabolic process / regulation of neuron projection development / regulation of cell differentiation / protein autoprocessing / collagen catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / intercellular bridge / myelination / protein maturation / secretory granule / central nervous system development / response to wounding / nuclear membrane / serine-type endopeptidase activity / nucleolus / endoplasmic reticulum / mitochondrion / extracellular space / extracellular region / nucleoplasm / cytoplasm
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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGomis-Ruth, F.X. / Bayes, A. / Sotiropoulou, G. / Pampalakis, G. / Tsetsenis, T. / Villegas, V. / Aviles, F.X. / Coll, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The Structure of Human Prokallikrein 6 Reveals a Novel Activation Mechanism for the Kallikrein Family.
Authors: Gomis-Ruth, F.X. / Bayes, A. / Sotiropoulou, G. / Pampalakis, G. / Tsetsenis, T. / Villegas, V. / Aviles, F.X. / Coll, M.
History
DepositionFeb 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "AB" ON SHEET RECORDS BELOW ARE ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "AB" ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS. THESE ARE REPRESENTED BY 8-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KALLIKREIN 6


Theoretical massNumber of molelcules
Total (without water)24,5181
Polymers24,5181
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.000, 66.400, 71.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein KALLIKREIN 6 / HUMAN PROKALLIKREIN 6 / PROTEASE M / NEUROSIN / ZYME


Mass: 24517.838 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / Strain (production host): PPIC9 / References: UniProt: Q92876
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES: ARG 19 GLN, ARG 80 GLN, ASN 134 GLN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 %PEG40001reservoir
20.1 MTris-HCl1reservoirpH8.5
30.2 M1reservoirMgCl2
410 mg/mlprotein1drop
510 mMTris-HCl1droppH8.5
610 mMbenzamidine1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934
DetectorType: ADSC/MAR RESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→38.6 Å / Num. obs: 19445 / % possible obs: 94 % / Redundancy: 3.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 4.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.7 / % possible all: 90.1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 64722
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 90.1 %

-
Processing

Software
NameVersionClassification
CNS1refinement
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NPM

1npm


Resolution: 1.8→33.2 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: CHYMOTRYPSINOGEN A (CTGA) NUMBERING APPLIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1418 7 %RANDOM
Rwork0.185 ---
obs0.185 19442 94 %-
Refinement stepCycle: LAST / Resolution: 1.8→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 0 158 1874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.39
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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