[English] 日本語
Yorodumi
- PDB-9hr1: Crystal structure of GH19 domain of D29-LysA (Form II) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hr1
TitleCrystal structure of GH19 domain of D29-LysA (Form II)
ComponentsEndolysin A
KeywordsHYDROLASE / GH19 / Peptidoglycan hydrolase / D29-LysA
Function / homology: / Hydrolases / viral release from host cell by cytolysis / Lysozyme-like domain superfamily / defense response to bacterium / hydrolase activity / ALANINE / Endolysin A
Function and homology information
Biological speciesMycobacterium phage D29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGalvez-Larrosa, L. / Ceballos-Zuniga, F. / Perez-Dorado, I.
Funding support Spain, 2items
OrganizationGrant numberCountry
Comunidad de Madrid2019-T1/BMD-14774 Spain
Spanish National Research Council202380E208 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Dissecting the molecular basis underlying mycobacterial cell-wall hydrolysis by the catalytic domains of D29LysA and DS6ALysA phage endolysins.
Authors: Ceballos-Zuniga, F. / Galvez-Larrosa, L. / Munoz, I.G. / Infantes, L. / Fernandez-Carrillo, J. / Perez-Dorado, I.
History
DepositionDec 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endolysin A
B: Endolysin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,03210
Polymers43,2862
Non-polymers7468
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint14 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.606, 89.052, 113.391
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

-
Protein , 1 types, 2 molecules AB

#1: Protein Endolysin A / Gene 10 protein / Gp10 / Lysis protein / Lysozyme


Mass: 21643.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: In both chains: GP N-terminal residues of a PreScission protease cleavage site. GH19 domain of D29-LysA (from 179 to 370)
Source: (gene. exp.) Mycobacterium phage D29 (virus) / Gene: 10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O64203, Hydrolases

-
Non-polymers , 5 types, 363 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12% (v/v) ethylene glycol; 6 % (w/v) PEG 8K, 0.1 M imidazole/MES buffer pH 6.5, and DL-amino-acids (glutamic acid, alanine, glycine; lysine, serine) at 20 mM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→113.39 Å / Num. obs: 30434 / % possible obs: 96.9 % / Redundancy: 14.3 % / Biso Wilson estimate: 26.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 15 % / Rmerge(I) obs: 0.895 / Num. unique obs: 2255 / CC1/2: 0.88 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→70.04 Å / SU ML: 0.1711 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2045 1549 5.1 %
Rwork0.1676 28819 -
obs0.1695 30368 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.4 Å2
Refinement stepCycle: LAST / Resolution: 2→70.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 44 355 3431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583170
X-RAY DIFFRACTIONf_angle_d0.73524312
X-RAY DIFFRACTIONf_chiral_restr0.0453465
X-RAY DIFFRACTIONf_plane_restr0.0105567
X-RAY DIFFRACTIONf_dihedral_angle_d12.57051180
LS refinement shellResolution: 2→2.06 Å
RfactorNum. reflection% reflection
Rfree0.2391 129 -
Rwork0.2133 2677 -
obs--99.96 %

+
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