[English] 日本語
Yorodumi
- PDB-7d55: Crystal structure of lys170 CBD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d55
TitleCrystal structure of lys170 CBD
ComponentsPutative N-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / lysin
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan turnover / peptidoglycan catabolic process / cell wall organization / killing of cells of another organism / defense response to bacterium
Similarity search - Function
: / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
Similarity search - Domain/homology
N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesEnterococcus phage phiM1EF22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.397 Å
AuthorsZhen, X.
CitationJournal: Eur.Biophys.J. / Year: 2021
Title: Structural and biochemical analyses of the tetrameric cell binding domain of Lys170 from enterococcal phage F170/08.
Authors: Xu, X. / Zhang, D. / Zhou, B. / Zhen, X. / Ouyang, S.
History
DepositionSep 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 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: Putative N-acetylmuramoyl-L-alanine amidase
B: Putative N-acetylmuramoyl-L-alanine amidase
C: Putative N-acetylmuramoyl-L-alanine amidase
D: Putative N-acetylmuramoyl-L-alanine amidase


Theoretical massNumber of molelcules
Total (without water)41,5644
Polymers41,5644
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-50 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.271, 93.838, 119.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

-
Components

#1: Protein
Putative N-acetylmuramoyl-L-alanine amidase


Mass: 10390.896 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus phage phiM1EF22 (virus) / Gene: PHIM1EF22_0110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z6FZW5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 25% (w/v) PEG 5000 and 1% (w/v) benzamidine hydrochloride
PH range: 6.5-9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.397→73.9411 Å / Num. obs: 58593 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.998 / Net I/σ(I): 2.7
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 573 / CC1/2: 0.909

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.397→73.941 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1969 1999 3.41 %
Rwork0.1665 56552 -
obs0.1675 58551 70.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.2 Å2 / Biso mean: 18.8309 Å2 / Biso min: 4.46 Å2
Refinement stepCycle: final / Resolution: 1.397→73.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 0 399 3275
Biso mean---33.21 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053001
X-RAY DIFFRACTIONf_angle_d0.754079
X-RAY DIFFRACTIONf_chiral_restr0.08419
X-RAY DIFFRACTIONf_plane_restr0.007522
X-RAY DIFFRACTIONf_dihedral_angle_d2.6621652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.397-1.4320.4684130.34583676
1.432-1.47070.3878180.2785259
1.4707-1.5140.2424310.238486315
1.514-1.56290.2989730.236206137
1.5629-1.61870.26641330.2057376466
1.6187-1.68350.2331500.1856428475
1.6835-1.76020.19531700.1929478684
1.7602-1.8530.21891880.1825528893
1.853-1.96910.21792010.16185695100
1.9691-2.12110.19012010.15135692100
2.1211-2.33460.18222010.16045719100
2.3346-2.67240.20382040.16715741100
2.6724-3.3670.18712040.16765800100
3.367-73.9410.17792120.15395967100

+
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