[English] 日本語
Yorodumi
- PDB-3hdf: Crystal structure of truncated endolysin R21 from phage 21 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hdf
TitleCrystal structure of truncated endolysin R21 from phage 21
ComponentsLysozyme
KeywordsHYDROLASE / lysozyme-like / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Late protein
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / host cell plasma membrane / membrane
Similarity search - Function
SAR-endolysin-like / : / Lysozyme - #40 / Endolysin T4 type / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / SAR-endolysin
Similarity search - Component
Biological speciesEnterobacteria phage P21 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsSun, Q. / Sacchettini, J.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Regulation of a muralytic enzyme by dynamic membrane topology.
Authors: Sun, Q. / Kuty, G.F. / Arockiasamy, A. / Xu, M. / Young, R. / Sacchettini, J.C.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _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: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,64918
Polymers31,4762
Non-polymers1,17316
Water5,585310
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3538
Polymers15,7381
Non-polymers6157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,29610
Polymers15,7381
Non-polymers5589
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.190, 109.673, 45.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Lysozyme / Lysis protein / Muramidase / Endolysin


Mass: 15738.151 Da / Num. of mol.: 2 / Fragment: UNP residues 27-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P21 (virus) / Gene: R / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27359, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsACCORDING TO THE AUTHORS RESIDUES PHE 105 AND VAL 106 ARE CORRECT IN THE PDB FILE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Bis-Tris propane, 2.5M sodium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2008
Details: Si(111) Double Crystal Monochromator. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 35740 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.038 / Χ2: 1.14 / Net I/σ(I): 44.163
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.766.10.37234880.8561100
1.76-1.836.10.27535420.9151100
1.83-1.916.10.19435281.0321100
1.91-2.026.10.13335231.2171100
2.02-2.146.10.135471.3981100
2.14-2.316.10.06835421.2681100
2.31-2.546.20.0535721.0871100
2.54-2.916.10.04835931.4961100
2.91-3.666.10.0336201.2641100
3.66-505.80.0237850.851198.9

-
Phasing

PhasingMethod: SIRAS

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→34.793 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.801 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.231 1820 5.1 %
Rwork0.2 33895 -
obs-35715 99.84 %
Solvent computationBsol: 63.425 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 86.53 Å2 / Biso mean: 28.309 Å2 / Biso min: 12.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.423 Å20 Å2-0 Å2
2--0.344 Å2-0 Å2
3----4.821 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 76 310 2459
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.6471
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONf_chiral_restr0.0491
X-RAY DIFFRACTIONf_dihedral_angle_d8.3691
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.0651
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.7-1.7080.247486X-RAY DIFFRACTION6894
1.708-1.7170.254485X-RAY DIFFRACTION6895
1.717-1.7260.251517X-RAY DIFFRACTION6896
1.726-1.7350.246497X-RAY DIFFRACTION6895
1.735-1.7440.228487X-RAY DIFFRACTION6895
1.744-1.7530.241475X-RAY DIFFRACTION6896
1.753-1.7630.228471X-RAY DIFFRACTION6895
1.763-1.7720.244503X-RAY DIFFRACTION6894
1.772-1.7820.227516X-RAY DIFFRACTION6896
1.782-1.7930.224484X-RAY DIFFRACTION6894
1.793-1.8030.243491X-RAY DIFFRACTION6896
1.803-1.8140.21484X-RAY DIFFRACTION6895
1.814-1.8250.225480X-RAY DIFFRACTION6893
1.825-1.8360.221497X-RAY DIFFRACTION6896
1.836-1.8470.204498X-RAY DIFFRACTION6896
1.847-1.8590.228476X-RAY DIFFRACTION6896
1.859-1.8710.223525X-RAY DIFFRACTION6895
1.871-1.8830.221498X-RAY DIFFRACTION6896
1.883-1.8960.222487X-RAY DIFFRACTION6895
1.896-1.9090.211477X-RAY DIFFRACTION6895
1.909-1.9230.207479X-RAY DIFFRACTION6894
1.923-1.9360.202485X-RAY DIFFRACTION6895
1.936-1.9510.202524X-RAY DIFFRACTION6894
1.951-1.9650.206484X-RAY DIFFRACTION6896
1.965-1.9810.19479X-RAY DIFFRACTION6894
1.981-1.9960.201495X-RAY DIFFRACTION6895
1.996-2.0120.195512X-RAY DIFFRACTION6895
2.012-2.0290.199465X-RAY DIFFRACTION6895
2.029-2.0460.19502X-RAY DIFFRACTION6894
2.046-2.0640.185491X-RAY DIFFRACTION6894
2.064-2.0820.195497X-RAY DIFFRACTION6895
2.082-2.1010.189468X-RAY DIFFRACTION6894
2.101-2.1210.2508X-RAY DIFFRACTION6896
2.121-2.1420.19497X-RAY DIFFRACTION6893
2.142-2.1630.2483X-RAY DIFFRACTION6895
2.163-2.1850.174490X-RAY DIFFRACTION6895
2.185-2.2090.181486X-RAY DIFFRACTION6894
2.209-2.2330.196501X-RAY DIFFRACTION6894
2.233-2.2580.186501X-RAY DIFFRACTION6896
2.258-2.2850.188497X-RAY DIFFRACTION6895
2.285-2.3130.183496X-RAY DIFFRACTION6896
2.313-2.3420.192484X-RAY DIFFRACTION6894
2.342-2.3730.192525X-RAY DIFFRACTION6895
2.373-2.4050.191488X-RAY DIFFRACTION6896
2.405-2.440.197494X-RAY DIFFRACTION6894
2.44-2.4760.187500X-RAY DIFFRACTION6895
2.476-2.5150.192504X-RAY DIFFRACTION6895
2.515-2.5560.2488X-RAY DIFFRACTION6896
2.556-2.60.196510X-RAY DIFFRACTION6895
2.6-2.6470.213508X-RAY DIFFRACTION6896
2.647-2.6980.197506X-RAY DIFFRACTION6896
2.698-2.7530.217483X-RAY DIFFRACTION6894
2.753-2.8130.213520X-RAY DIFFRACTION6893
2.813-2.8790.208476X-RAY DIFFRACTION6894
2.879-2.9510.192513X-RAY DIFFRACTION6896
2.951-3.030.199512X-RAY DIFFRACTION6895
3.03-3.1190.199500X-RAY DIFFRACTION6895
3.119-3.220.176510X-RAY DIFFRACTION6895
3.22-3.3350.193489X-RAY DIFFRACTION6894
3.335-3.4680.177535X-RAY DIFFRACTION6896
3.468-3.6260.165502X-RAY DIFFRACTION6896
3.626-3.8170.148516X-RAY DIFFRACTION6895
3.817-4.0560.155506X-RAY DIFFRACTION6893
4.056-4.3690.164509X-RAY DIFFRACTION6894
4.369-4.8070.186507X-RAY DIFFRACTION6893
4.807-5.50.194533X-RAY DIFFRACTION6896
5.5-6.9210.253541X-RAY DIFFRACTION6896
6.921-34.8010.253562X-RAY DIFFRACTION6891

+
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