[English] 日本語
Yorodumi
- PDB-1xov: The crystal structure of the listeria monocytogenes bacteriophage... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xov
TitleThe crystal structure of the listeria monocytogenes bacteriophage PSA endolysin PlyPSA
ComponentsPly protein
KeywordsHYDROLASE / alpha/beta hydrolase / multi-domain
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / methyltransferase activity / helicase activity / methylation / metal ion binding
Similarity search - Function
PSA endolysin, cell wall binding domain / PSA endolysin C-terminal cell wall binding domain / Zn-dependent exopeptidases / : / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / SH3 Domains / Aminopeptidase / SH3 type barrels. ...PSA endolysin, cell wall binding domain / PSA endolysin C-terminal cell wall binding domain / Zn-dependent exopeptidases / : / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / SH3 Domains / Aminopeptidase / SH3 type barrels. / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / LYSINE / Ply protein
Similarity search - Component
Biological speciesListeria phage PSA (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKorndoerfer, I.P. / Skerra, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The crystal structure of the bacteriophage PSA endolysin reveals a unique fold responsible for specific recognition of Listeria cell walls
Authors: Korndoerfer, I.P. / Danzer, J. / Schmelcher, M. / Zimmer, M. / Skerra, A. / Loessner, M.J.
History
DepositionOct 7, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 3, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Ply protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2597
Polymers36,6461
Non-polymers6136
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.586, 90.586, 213.667
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2234-

HOH

21A-2292-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Ply protein / plypsa


Mass: 36645.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria phage PSA (virus) / Species: Listeria phage 2389 / Description: host: Listeria monocytogenes / Gene: ply / Plasmid: psplpsa / Production host: Escherichia coli (E. coli) / Strain (production host): JM83
References: UniProt: Q8W5Y8, N-acetylmuramoyl-L-alanine amidase

-
Non-polymers , 7 types, 313 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#7: 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 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsRESIDUES GLU 2001 AND LYS 2002 ARE UNIDENTIFIED COPURIFIED PEPTIDE. THIS PEPTIDE IS POSSIBLY ...RESIDUES GLU 2001 AND LYS 2002 ARE UNIDENTIFIED COPURIFIED PEPTIDE. THIS PEPTIDE IS POSSIBLY DEGRADATION OR AUTOPROTEOLYSIS PRODUCT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 100mM hepes, 0.2M (nh4)2so4, 25% peg 3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.92 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 2, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 48970 / Num. obs: 48940 / % possible obs: 99.92 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 18.79 % / Biso Wilson estimate: 27.08 Å2 / Rsym value: 0.08 / Net I/σ(I): 5.34
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 17 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.05 / Num. unique all: 7005 / Rsym value: 0.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.791 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The data used for refinement is from a native crystal which was only measured a 0.92 A.
RfactorNum. reflection% reflectionSelection details
Rfree0.19831 2442 5 %RANDOM
Rwork0.17023 ---
obs0.17164 46406 99.91 %-
all-46406 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0.64 Å20 Å2
2---1.29 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 33 307 2828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222570
X-RAY DIFFRACTIONr_bond_other_d0.0010.022299
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9443457
X-RAY DIFFRACTIONr_angle_other_deg0.78535386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.624.206107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1315478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1391511
X-RAY DIFFRACTIONr_chiral_restr0.1230.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022808
X-RAY DIFFRACTIONr_gen_planes_other00.02511
X-RAY DIFFRACTIONr_nbd_refined0.220.3485
X-RAY DIFFRACTIONr_nbd_other0.210.32210
X-RAY DIFFRACTIONr_nbtor_refined0.1880.51230
X-RAY DIFFRACTIONr_nbtor_other0.0930.51461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.5327
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0370.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.551
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.26821998
X-RAY DIFFRACTIONr_mcbond_other0.5352654
X-RAY DIFFRACTIONr_mcangle_it2.67132508
X-RAY DIFFRACTIONr_scbond_it2.20921234
X-RAY DIFFRACTIONr_scangle_it2.9173949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 164 -
Rwork0.202 3388 -
obs-3552 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.08060.24170.14512.63390.02142.016-0.08840.15590.13080.17220.08610.0991-0.0552-0.05110.0023-0.09020.01890.0338-0.13870.077-0.321979.82914.57410.273
23.939-1.80030.74911.3973-0.28750.5225-0.0272-0.0543-0.2725-0.04060.07180.17510.0309-0.0397-0.04460.0040.00130.00550.02130.11170.076941.96634.5930.587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 17812 - 190
2X-RAY DIFFRACTION2AA179 - 314191 - 326

+
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