[English] 日本語
Yorodumi
- PDB-2y2e: crystal structure of AmpD grown at pH 5.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y2e
Titlecrystal structure of AmpD grown at pH 5.5
Components1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
KeywordsHYDROLASE / PEPTIDOGLYCAN AMIDASE / AMIDASE_2 FAMILY / ACTIVATION MECHANISM
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / cell wall organization / metal ion binding / cytoplasm
Similarity search - Function
Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD
Similarity search - Component
Biological speciesCITROBACTER FREUNDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCarrasco-Lopez, C. / Rojas-Altuve, A. / Zhang, W. / Hesek, D. / Lee, M. / Barbe, S. / Andre, I. / Silva-Martin, N. / Martinez-Ripoll, M. / Mobashery, S. / Hermoso, J.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structures of Bacterial Peptidoglycan Amidase Ampd and an Unprecedented Activation Mechanism.
Authors: Carrasco-Lopez, C. / Rojas-Altuve, A. / Zhang, W. / Hesek, D. / Lee, M. / Barbe, S. / Andre, I. / Ferrer, P. / Silva-Martin, N. / Castro, G.R. / Martinez-Ripoll, M. / Mobashery, S. / Hermoso, J.A.
History
DepositionDec 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
B: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
C: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8106
Polymers62,6143
Non-polymers1963
Water14,898827
1
A: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9372
Polymers20,8711
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9372
Polymers20,8711
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9372
Polymers20,8711
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.982, 67.982, 93.125
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein 1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD / AMPD / N-ACETYLMURAMOYL-L-ALANINE AMIDASE


Mass: 20871.361 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: AMPD PH 5.5 / Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P82974, N-acetylmuramoyl-L-alanine amidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 827 / 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 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 5.5 / Details: 0.1 M TRIS PH 5.5, 0.1 M LI2SO4, 28% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→46.5 Å / Num. obs: 32782 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y28

2y28


Resolution: 2→36.521 Å / SU ML: 0.32 / σ(F): 0.05 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 2300 7.2 %
Rwork0.2011 --
obs0.2062 32182 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.897 Å2 / ksol: 0.393 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3342 Å20 Å20 Å2
2--2.3342 Å20 Å2
3----4.6683 Å2
Refinement stepCycle: LAST / Resolution: 2→36.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4231 0 3 827 5061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114370
X-RAY DIFFRACTIONf_angle_d1.1155976
X-RAY DIFFRACTIONf_dihedral_angle_d17.6531546
X-RAY DIFFRACTIONf_chiral_restr0.075631
X-RAY DIFFRACTIONf_plane_restr0.006797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.28212170.21212901X-RAY DIFFRACTION97
2.0715-2.15440.29932170.20482953X-RAY DIFFRACTION98
2.1544-2.25250.322320.20622979X-RAY DIFFRACTION98
2.2525-2.37120.28272620.20812955X-RAY DIFFRACTION99
2.3712-2.51980.29812150.20183060X-RAY DIFFRACTION99
2.5198-2.71420.29012300.19172971X-RAY DIFFRACTION100
2.7142-2.98730.26672150.20243028X-RAY DIFFRACTION100
2.9873-3.41930.2642350.19133026X-RAY DIFFRACTION100
3.4193-4.30680.23612350.18173015X-RAY DIFFRACTION100
4.3068-36.52710.23452420.21162994X-RAY DIFFRACTION100

+
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