[English] 日本語
Yorodumi
- PDB-4pia: Crystal structure of S. Aureus Autolysin E -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pia
TitleCrystal structure of S. Aureus Autolysin E
ComponentsAutolysin E
KeywordsHYDROLASE / autolysin / glycosidase / peptidoglycan
Function / homology
Function and homology information


amidase activity / membrane => GO:0016020 / extracellular region / membrane
Similarity search - Function
: / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
Similarity search - Domain/homology
Autolysin E (1e-98,63%,84%,258-258) / Autolysin E (1e-98,63%,84%,258-258)
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.466 Å
AuthorsMihelic, M. / Renko, M. / Dobersek, A. / Bedrac, L. / Turk, D.
CitationJournal: Iucrj / Year: 2017
Title: The mechanism behind the selection of two different cleavage sites in NAG-NAM polymers
Authors: Mihelic, M. / Vlahovicek-Kahlina, K. / Renko, M. / Mesnage, S. / Dobersek, A. / Taler-Vercic, A. / Jakas, A. / Turk, D.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Autolysin E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38710
Polymers26,0681
Non-polymers3199
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-71 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.599, 69.927, 73.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Autolysin E


Mass: 26068.279 Da / Num. of mol.: 1 / Fragment: UNP residues 35-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: SAV2307 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99RW6, UniProt: A0A0H3JT72*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2 M (NH4)2SO4, 2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→23 Å / Num. obs: 41563 / % possible obs: 99.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.043 / Χ2: 0.655 / Net I/av σ(I): 33.475 / Net I/σ(I): 39.2 / Num. measured all: 229537
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.46-1.4940.29112640.80295.97
1.49-1.515.30.25920800.60799.4
1.51-1.545.50.21420830.56100
1.54-1.575.50.18520770.51899.8
1.57-1.615.50.1621050.48899.8
1.61-1.645.50.13920860.481100
1.64-1.695.50.11820950.50899.9
1.69-1.735.50.10920860.542100
1.73-1.785.60.09421040.51199.9
1.78-1.845.60.0821030.526100
1.84-1.915.60.06820900.557100
1.91-1.985.60.05821170.608100
1.98-2.075.70.04720930.609100
2.07-2.185.70.04221230.639100
2.18-2.325.70.03821300.68100
2.32-2.55.70.03621400.708100
2.5-2.755.70.03321410.731100
2.75-3.145.70.03121450.847100
3.14-3.965.60.02821951.031100
3.96-235.30.03123061.171100

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
RefinementResolution: 1.466→23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1694 / WRfactor Rwork: 0.1445 / FOM work R set: 0.9053 / SU B: 0.862 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0583 / SU Rfree: 0.0594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1715 2090 5 %RANDOM
Rwork0.1492 39382 --
obs0.1503 41472 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.62 Å2 / Biso mean: 15.919 Å2 / Biso min: 5.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.466→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 9 258 2076
Biso mean--22.08 28.17 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021883
X-RAY DIFFRACTIONr_bond_other_d0.0010.021789
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.9472533
X-RAY DIFFRACTIONr_angle_other_deg0.88134140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1435237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29425.61298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65315364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.097158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
X-RAY DIFFRACTIONr_mcbond_it1.5311.297912
X-RAY DIFFRACTIONr_mcbond_other1.5081.295911
X-RAY DIFFRACTIONr_mcangle_it2.3541.9371140
LS refinement shellResolution: 1.466→1.504 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 152 -
Rwork0.195 2730 -
all-2882 -
obs--94.65 %

+
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