[English] 日本語
Yorodumi
- PDB-5wqw: X-ray structure of catalytic domain of autolysin from Clostridium... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wqw
TitleX-ray structure of catalytic domain of autolysin from Clostridium perfringens
ComponentsN-acetylglucosaminidase
KeywordsHYDROLASE / autolysin / glycoside hydrolase 73 family
Function / homology
Function and homology information


peptidoglycan N-acetylglucosaminidase activity / amidase activity
Similarity search - Function
: / Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / SH3-like domain, bacterial-type / SH3-like domain superfamily
Similarity search - Domain/homology
N-acetylglucosaminidase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.76 Å
AuthorsTamai, E. / Sekiya, H. / Goda, E. / Makihata, N. / Maki, J. / Yoshida, H. / Kamitori, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHIJP15K06973, JP15K08482 Japan
CitationJournal: FEBS Lett. / Year: 2017
Title: Structural and biochemical characterization of the Clostridium perfringens autolysin catalytic domain
Authors: Tamai, E. / Sekiya, H. / Goda, E. / Makihata, N. / Maki, J. / Yoshida, H. / Kamitori, S.
History
DepositionNov 29, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 7, 2016ID: 5AZM
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Mar 20, 2024Group: 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: N-acetylglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9497
Polymers30,5761
Non-polymers3726
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint21 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.320, 37.170, 64.000
Angle α, β, γ (deg.)90.00, 100.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein N-acetylglucosaminidase / Probable surface protein


Mass: 30576.330 Da / Num. of mol.: 1 / Fragment: autolysin catalytic domain, UNP residues 871-1129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria)
Strain: 13 / Type A / Gene: CPE1231 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XL11
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.06 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1M CHES PH9.5, 10% (W/V) PEG 3000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→42.87 Å / Num. obs: 22481 / % possible obs: 96 % / Redundancy: 3.68 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / CC1/2: 0.852 / % possible all: 91.4

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.76→42.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.09 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.19249 1158 5.2 %RANDOM
Rwork0.16072 ---
obs0.16241 21323 96.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å2-0.52 Å2
2---0.98 Å20 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.76→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 24 121 2159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022079
X-RAY DIFFRACTIONr_bond_other_d00.021949
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9382809
X-RAY DIFFRACTIONr_angle_other_deg0.63334460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.095253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17424.44499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42915336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.411159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022397
X-RAY DIFFRACTIONr_gen_planes_other00.02520
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 70 -
Rwork0.224 1480 -
obs--91.12 %

+
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