[English] 日本語
Yorodumi
- PDB-3d2y: Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d2y
TitleComplex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the substrate anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
Components
  • Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
  • N-acetylmuramoyl-L-alanine amidase amiD
KeywordsHYDROLASE / ZINC AMIDASE / PGRP / Peptidoglycan Recognizing Protein / AmpD / N-ACETYLMURAMYL-L-ALANINE AMIDASE / Cell wall biogenesis/degradation / Lipoprotein / Membrane / Metal-binding / Outer membrane / Palmitate
Function / homology
Function and homology information


N-acetyl-anhydromuramoyl-L-alanine amidase activity / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan turnover / outer membrane / peptidoglycan catabolic process / cell outer membrane / cell wall organization / zinc ion binding
Similarity search - Function
Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / : / PGBD superfamily / 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 ...Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / : / PGBD superfamily / 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 / PGBD-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-acetylmuramoyl-L-alanine amidase AmiD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKerff, F. / Petrella, S. / Herman, R. / Sauvage, E. / Mercier, F. / Luxen, A. / Frere, J.M. / Joris, B. / Charlier, P.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Specific Structural Features of the N-Acetylmuramoyl-l-Alanine Amidase AmiD from Escherichia coli and Mechanistic Implications for Enzymes of This Family.
Authors: Kerff, F. / Petrella, S. / Mercier, F. / Sauvage, E. / Herman, R. / Pennartz, A. / Zervosen, A. / Luxen, A. / Frere, J.M. / Joris, B. / Charlier, P.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: N-acetylmuramoyl-L-alanine amidase amiD
B: Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1654
Polymers29,9812
Non-polymers1842
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetylmuramoyl-L-alanine amidase amiD
B: Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
hetero molecules

A: N-acetylmuramoyl-L-alanine amidase amiD
B: Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3308
Polymers59,9624
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area6370 Å2
ΔGint-3 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.274, 88.274, 181.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

DetailsThe biological assembly is a monomer but the protein is found as a dimer in the crystal with a swapping of the N-terminus

-
Components

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


Mass: 29376.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 MG1655 / Gene: amiD, ybjR, b0867, JW0851 / Plasmid: pBAD/Myc-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
References: UniProt: P75820, N-acetylmuramoyl-L-alanine amidase
#2: Protein/peptide Anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys


Mass: 604.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 3.41 Å3/Da / Density % sol: 63.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1M LiCl, 10 % PEG 6K, 0.1M ZnCl2, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97885 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 1.75→47.5 Å / Num. obs: 42426 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.6
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5643 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BGX

2bgx
PDB Unreleased entry


Resolution: 1.75→44.15 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.354 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25326 2136 5 %RANDOM
Rwork0.2069 ---
obs0.20919 40210 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.923 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 12 308 2418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222198
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9673000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5825266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.923.704108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66915350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6631518
X-RAY DIFFRACTIONr_chiral_restr0.1110.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021709
X-RAY DIFFRACTIONr_nbd_refined0.1960.21033
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.228
X-RAY DIFFRACTIONr_mcbond_it2.50921366
X-RAY DIFFRACTIONr_mcangle_it3.19732137
X-RAY DIFFRACTIONr_scbond_it2.7992962
X-RAY DIFFRACTIONr_scangle_it3.9243858
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 169 -
Rwork0.283 2620 -
obs-2186 89.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
123.01253.78070.445316.2316-6.6932.9413-1.0101-0.90690.3139-0.0810.2557-1.0070.6546-0.88560.75440.17550.2044-0.04820.0834-0.19590.158239.95413.92664.299
20.47180.40560.76370.48591.02212.21030.03890.0549-0.08830.08640.1163-0.20490.08080.2517-0.15520.01480.057-0.04280.075-0.0420.002736.21435.83784.369
31.7369-0.05631.38950.1626-0.2061.30470.0320.0688-0.03060.00540.0001-0.01260.06240.1134-0.0320.01710.0329-0.03450.0511-0.026-0.003134.90139.33686.843
437.16620.9934-23.616552.562126.915530.13031.0823-0.40012.25171.55-1.22731.6493-0.6493-1.38310.1450.17790.2256-0.03710.0839-0.19220.154427.14457.295103.599
51.7437-0.5612-0.18011.18891.22673.1218-0.07990.0427-0.018-0.04230.0447-0.162-0.24260.17160.0352-0.01940.0043-0.05210.0609-0.02030.005242.99448.39687.982
61.0927-0.59760.35890.4999-0.18871.4781-0.19140.05240.19830.06930.0337-0.0969-0.27610.18050.15770.0662-0.0397-0.09670.0182-0.0020.033632.04157.94181.678
71.9767-0.10710.34041.2552-0.61592.0199-0.17-0.07840.07980.08220.11150.1086-0.2191-0.13810.05850.06930.0594-0.05850.0064-0.0117-0.008619.17357.5983.23
81.7769-1.0616-0.16651.57450.18142.7197-0.15860.16080.31610.0193-0.1185-0.1628-0.5816-0.04490.2770.08620.0051-0.1235-0.05080.02720.030626.89962.5779.582
911.44482.85927.65234.90665.771616.20910.0507-0.59370.1170.5198-0.14340.07380.2098-0.39690.09270.06640.026-0.01250.0830.01720.005325.32839.05692.67
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 136 - 13
2X-RAY DIFFRACTION2AA14 - 6514 - 65
3X-RAY DIFFRACTION3AA66 - 10866 - 108
4X-RAY DIFFRACTION4AA109 - 118109 - 118
5X-RAY DIFFRACTION5AA119 - 140119 - 140
6X-RAY DIFFRACTION6AA141 - 198141 - 198
7X-RAY DIFFRACTION7AA199 - 235199 - 235
8X-RAY DIFFRACTION8AA236 - 261236 - 261
9X-RAY DIFFRACTION9BB1 - 41 - 4

+
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