[English] 日本語
Yorodumi
- PDB-7zoc: Crystal structure of the peptidase domain of collagenase H from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zoc
TitleCrystal structure of the peptidase domain of collagenase H from Clostridium histolyticum in complex with N-aryl-2-alkylmercaptoacetamide-based inhibitor
ComponentsCollagenase ColH
KeywordsHYDROLASE / Collagenase / Inhibitor / complex
Function / homology
Function and homology information


tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / 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 / PKD domain / Polycystic kidney disease (PKD) domain profile. ...Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / 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 / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
~{N}-(4-ethanoylphenyl)-2-sulfanyl-propanamide / Collagenase ColH
Similarity search - Component
Biological speciesHathewaya histolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsSchoenauer, E. / Brandstetter, H.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP31843 Austria
CitationJournal: To Be Published
Title: N-aryl-2-iso-butylmercaptoacetamides: the discovery of highly potent and selective inhibitors of P. aeruginosa virulence factor LasB and C. histolyticum virulence factor ColH
Authors: Schoenauer, E. / Brandstetter, H.
History
DepositionApr 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Collagenase ColH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4234
Polymers48,0941
Non-polymers3293
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.425, 81.981, 102.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Collagenase ColH / Class II collagenase / Gelatinase ColH / Microbial collagenase


Mass: 48094.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hathewaya histolytica (bacteria) / Gene: colH / Production host: Escherichia coli (E. coli) / References: UniProt: Q46085, microbial collagenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-T8E / ~{N}-(4-ethanoylphenyl)-2-sulfanyl-propanamide


Mass: 223.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: Hepes/MOPS pH 7.1, 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, MPD, PEG 1000, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.91→43.6 Å / Num. obs: 34338 / % possible obs: 99.49 % / Redundancy: 6.7 % / CC1/2: 0.996 / Net I/σ(I): 10.58
Reflection shellResolution: 1.91→1.98 Å / Num. unique obs: 3357 / CC1/2: 0.889

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.19rc5_4047refinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O7E

5o7e


Resolution: 1.91→43.6 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 1759 5.13 %
Rwork0.1987 32562 -
obs-34321 99.5 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.34 Å2
Refinement stepCycle: LAST / Resolution: 1.91→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 17 279 3360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01053168
X-RAY DIFFRACTIONf_angle_d1.02524293
X-RAY DIFFRACTIONf_chiral_restr0.0633442
X-RAY DIFFRACTIONf_plane_restr0.0087566
X-RAY DIFFRACTIONf_dihedral_angle_d5.6428442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.42211280.35672452X-RAY DIFFRACTION99.5
1.96-2.020.36411230.28812492X-RAY DIFFRACTION99.77
2.02-2.080.31741250.24962460X-RAY DIFFRACTION99.54
2.08-2.160.29161360.23572476X-RAY DIFFRACTION99.58
2.16-2.250.29421530.22592443X-RAY DIFFRACTION99.35
2.25-2.350.26811210.20362530X-RAY DIFFRACTION99.62
2.35-2.470.2531250.20052484X-RAY DIFFRACTION99.69
2.47-2.630.24281240.21442484X-RAY DIFFRACTION99.66
2.63-2.830.27781460.21362514X-RAY DIFFRACTION99.96
2.83-3.110.26691350.21342505X-RAY DIFFRACTION99.36
3.11-3.560.21551420.19412520X-RAY DIFFRACTION99.25
3.56-4.490.20541460.15792546X-RAY DIFFRACTION99.7
4.49-43.60.19791550.16542656X-RAY DIFFRACTION98.6

+
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