[English] 日本語
Yorodumi
- PDB-2pic: E. coli lytic transglycosylase MltA-D308A in apo-2 form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pic
TitleE. coli lytic transglycosylase MltA-D308A in apo-2 form
ComponentsMembrane-bound lytic murein transglycosylase A
KeywordsHYDROLASE / double-psi beta-barrel / lytic transglycosylase / active site mutant
Function / homology
Function and homology information


: / lytic transglycosylase activity / peptidoglycan turnover / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / cell wall organization / cell outer membrane / outer membrane-bounded periplasmic space
Similarity search - Function
Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily / Ribosomal Protein L25; Chain P ...Barwin-like endoglucanases / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain / RlpA-like domain superfamily / Ribosomal Protein L25; Chain P / Barwin-like endoglucanases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Membrane-bound lytic murein transglycosylase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
Authorsvan Straaten, K.E. / Dijkstra, B.W. / Thunnissen, A.M.W.H.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structure of Escherichia coli Lytic transglycosylase MltA with bound chitohexaose: implications for peptidoglycan binding and cleavage
Authors: van Straaten, K.E. / Barends, T.R. / Dijkstra, B.W. / Thunnissen, A.M.W.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure
Authors: Barends, T.R.M. / de Jong, R.M. / van Straaten, K.E. / Thunnissen, A.M.W.H. / Dijkstra, B.W.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of MltA from Escherichia coli reveals a unique lytic transglycosylase fold
Authors: van Straaten, K.E. / Dijkstra, B.W. / Vollmer, W. / Thunnissen, A.M.W.H.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray analysis of the lytic transglycosylase MltA from Escherichia coli
Authors: van Straaten, K.E. / Dijkstra, B.W. / Thunnissen, A.M.W.H.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Membrane-bound lytic murein transglycosylase A


Theoretical massNumber of molelcules
Total (without water)38,2071
Polymers38,2071
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.9, 80.9, 130.3
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

-
Components

#1: Protein Membrane-bound lytic murein transglycosylase A / E.C.3.2.1.- / Murein hydrolase A / Mlt38


Mass: 38206.680 Da / Num. of mol.: 1 / Mutation: D308A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: mltA, mlt / Plasmid: pMSS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0A935, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.25-0.35M NaCl, 10mM magnesium chloride, 100mM sodium acetate buffer, pH 4.2, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 22884 / Num. obs: 22884 / % possible obs: 93.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Χ2: 1.046 / Net I/σ(I): 21.5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.330.3415841.292166
2.33-2.420.27720091.067184.1
2.42-2.530.25223581.119198.1
2.53-2.670.18123451.068198
2.67-2.830.12723591.017198.3
2.83-3.050.08923970.996198.7
3.05-3.360.06424200.981198.8
3.36-3.850.05224021.053198.2
3.85-4.840.0424431.02198.9
4.84-300.03825670.989198.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
ProDCdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AE0

2ae0


Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.265 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.245 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1155 5.1 %RANDOM
Rwork0.203 ---
all0.206 22709 --
obs0.206 22709 94.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.472 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.62 Å20 Å2
2--1.25 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 0 138 2778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212711
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.933670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.3975335
X-RAY DIFFRACTIONr_chiral_restr0.1050.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022163
X-RAY DIFFRACTIONr_nbd_refined0.190.31116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.549
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.53
X-RAY DIFFRACTIONr_mcbond_it3.2781.51663
X-RAY DIFFRACTIONr_mcangle_it5.0322655
X-RAY DIFFRACTIONr_scbond_it7.32231048
X-RAY DIFFRACTIONr_scangle_it10.0654.51015
LS refinement shellResolution: 2.25→2.273 Å / Total num. of bins used: 50
RfactorNum. reflection
Rfree0.44 23
Rwork0.325 407
obs-430

+
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