[English] 日本語
Yorodumi
- PDB-4epc: Crystal structure of Autolysin repeat domains from Staphylococcus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4epc
TitleCrystal structure of Autolysin repeat domains from Staphylococcus epidermidis
ComponentsN-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / SH3b Fold / Extracellular
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / N-acetylmuramoyl-L-alanine amidase / amidase activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / extracellular region
Similarity search - Function
SH3 type barrels. - #170 / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Ami_2 / N-acetylmuramoyl-L-alanine amidase ...SH3 type barrels. - #170 / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Bifunctional autolysin
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsZoll, S. / Stehle, T.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Ligand-binding properties and conformational dynamics of autolysin repeat domains in staphylococcal cell wall recognition.
Authors: Zoll, S. / Schlag, M. / Shkumatov, A.V. / Rautenberg, M. / Svergun, D.I. / Gotz, F. / Stehle, T.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetylmuramoyl-L-alanine amidase


Theoretical massNumber of molelcules
Total (without water)36,6481
Polymers36,6481
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.360, 95.360, 233.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein N-acetylmuramoyl-L-alanine amidase / / AtlE / R2ab


Mass: 36648.047 Da / Num. of mol.: 1 / Fragment: UNP residues 516-847
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Gene: atl, atlE / Production host: Escherichia coli (E. coli)
References: UniProt: O33635, N-acetylmuramoyl-L-alanine amidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES 514-695 ARE MISSING IN THE COORDINATES. IN THE CRYSTAL LATTICE, HALF OF THE PROTEIN ...RESIDUES 514-695 ARE MISSING IN THE COORDINATES. IN THE CRYSTAL LATTICE, HALF OF THE PROTEIN PROTRUDES INTO A LARGE SOLVENT CHANNEL VIA A FLEXIBLE LINKER AND IS DISORDERED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M LiSO4, 0.1 M CAPS, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→25.65 Å / Num. all: 14672 / Num. obs: 14506 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→2.98 Å / % possible all: 99.8

-
Processing

Software
NameVersionClassification
XDSdata scaling
SOLVEphasing
BUSTER2.10.0refinement
XDSdata reduction
RefinementMethod to determine structure: MIR / Resolution: 2.9→25.65 Å / Cor.coef. Fo:Fc: 0.7984 / Cor.coef. Fo:Fc free: 0.7783 / SU R Cruickshank DPI: 0.273 / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 973 6.71 %RANDOM
Rwork0.2633 ---
all0.2656 14672 --
obs0.2656 14506 99.11 %-
Displacement parametersBiso mean: 55.64 Å2
Baniso -1Baniso -2Baniso -3
1--16.2466 Å20 Å20 Å2
2---16.2466 Å20 Å2
3---32.4931 Å2
Refine analyzeLuzzati coordinate error obs: 0.493 Å
Refinement stepCycle: LAST / Resolution: 2.9→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 0 18 1223
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011229HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.231674HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d359SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes32HARMONIC2
X-RAY DIFFRACTIONt_gen_planes170HARMONIC5
X-RAY DIFFRACTIONt_it1229HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion19.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion165SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1242SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.13 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3032 188 6.49 %
Rwork0.2714 2708 -
all0.2734 2896 -
obs--99.11 %

+
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