[English] 日本語
Yorodumi
- PDB-8jt1: COLLAGENASE FROM GRIMONTIA (VIBRIO) HOLLISAE 1706B COMPLEXED WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jt1
TitleCOLLAGENASE FROM GRIMONTIA (VIBRIO) HOLLISAE 1706B COMPLEXED WITH GLY-PRO-HYP-GLY-PRO-HYP
Components
  • 6-mer peptide
  • Microbial collagenase
KeywordsHYDROLASE / GRIMONTIA HOLLISAE / COLLAGENASE
Function / homology
Function and homology information


microbial collagenase / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / microbial collagenase
Similarity search - Component
Biological speciesGrimontia hollisae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUeshima, S. / Yaskawa, K. / Takita, T. / Mikami, B.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22H03332 Japan
CitationJournal: Febs Lett. / Year: 2023
Title: Insights into the catalytic mechanism of Grimontia hollisae collagenase through structural and mutational analyses.
Authors: Ueshima, S. / Yasumoto, M. / Kitagawa, Y. / Akazawa, K. / Takita, T. / Tanaka, K. / Hattori, S. / Mizutani, K. / Mikami, B. / Yasukawa, K.
History
DepositionJun 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microbial collagenase
B: Microbial collagenase
C: 6-mer peptide
E: 6-mer peptide
F: 6-mer peptide
G: 6-mer peptide
I: 6-mer peptide
J: 6-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,472110
Polymers127,1188
Non-polymers6,354102
Water10,377576
1
A: Microbial collagenase
C: 6-mer peptide
E: 6-mer peptide
F: 6-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,66654
Polymers63,5594
Non-polymers3,10750
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microbial collagenase
G: 6-mer peptide
I: 6-mer peptide
J: 6-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,80656
Polymers63,5594
Non-polymers3,24752
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.017, 74.890, 135.134
Angle α, β, γ (deg.)90.000, 126.020, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein / Protein/peptide , 2 types, 8 molecules ABCEFGIJ

#1: Protein Microbial collagenase


Mass: 61901.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grimontia hollisae (bacteria) / Production host: Brevibacillus (bacteria) / References: UniProt: F7IZI6, microbial collagenase
#2: Protein/peptide
6-mer peptide


Mass: 552.578 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 7 types, 678 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 89 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M CALCIUM ACETATE, 0.1M MES SODIUM HYDROXIDE PH 6.0, 20% (W/V) POLYETHYLENE GLYCOL 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→37.44 Å / Num. obs: 96513 / % possible obs: 99.3 % / Redundancy: 3.85 % / Biso Wilson estimate: 29.85 Å2 / CC1/2: 0.898 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.093 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.96 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 15381 / CC1/2: 0.761 / Rrim(I) all: 0.762 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.44 Å / SU ML: 0.2122 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1705
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2136 4825 5 %
Rwork0.1759 91671 -
obs0.1778 96496 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.82 Å2
Refinement stepCycle: LAST / Resolution: 2→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8610 0 391 576 9577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00639235
X-RAY DIFFRACTIONf_angle_d0.786412425
X-RAY DIFFRACTIONf_chiral_restr0.04781285
X-RAY DIFFRACTIONf_plane_restr0.0061620
X-RAY DIFFRACTIONf_dihedral_angle_d15.10283190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.30851510.27482871X-RAY DIFFRACTION94.47
2.03-2.050.24491610.24643066X-RAY DIFFRACTION99.94
2.05-2.070.31051610.24053057X-RAY DIFFRACTION99.97
2.07-2.10.28671600.24223031X-RAY DIFFRACTION100
2.1-2.130.26471590.21983033X-RAY DIFFRACTION99.94
2.13-2.160.22641600.21823034X-RAY DIFFRACTION99.97
2.16-2.190.24811630.20423087X-RAY DIFFRACTION99.85
2.19-2.220.27111590.20093033X-RAY DIFFRACTION100
2.22-2.260.25061620.19473066X-RAY DIFFRACTION99.91
2.26-2.290.24941600.19583049X-RAY DIFFRACTION99.97
2.29-2.330.22361620.19483068X-RAY DIFFRACTION99.94
2.33-2.370.21761600.1873053X-RAY DIFFRACTION99.94
2.37-2.420.24631620.19543078X-RAY DIFFRACTION99.97
2.42-2.470.24011620.18143065X-RAY DIFFRACTION99.94
2.47-2.520.22991590.18273021X-RAY DIFFRACTION99.81
2.52-2.580.2111620.18633076X-RAY DIFFRACTION99.94
2.58-2.650.23431590.18313031X-RAY DIFFRACTION99.94
2.65-2.720.2521610.18223062X-RAY DIFFRACTION99.78
2.72-2.80.24821610.18043053X-RAY DIFFRACTION99.84
2.8-2.890.24181620.18363066X-RAY DIFFRACTION99.88
2.89-2.990.21681610.18283064X-RAY DIFFRACTION99.72
2.99-3.110.22081610.17523056X-RAY DIFFRACTION99.26
3.11-3.250.20551600.17643038X-RAY DIFFRACTION99.26
3.25-3.420.22181600.16583050X-RAY DIFFRACTION98.65
3.42-3.640.21831580.15593010X-RAY DIFFRACTION98.63
3.64-3.920.17081630.15263083X-RAY DIFFRACTION99.72
3.92-4.310.16531620.14613085X-RAY DIFFRACTION99.78
4.31-4.930.18111630.14283099X-RAY DIFFRACTION99.76
4.93-6.210.19311640.1793112X-RAY DIFFRACTION99.64
6.21-37.440.18671670.17043174X-RAY DIFFRACTION99.32

+
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://pdbjlvh1.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