[English] 日本語
Yorodumi
- PDB-5aa4: Crystal structure of MltF from Pseudomonas aeruginosa in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aa4
TitleCrystal structure of MltF from Pseudomonas aeruginosa in complex with cell-wall tetrapeptide
Components(MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F) x 2
KeywordsLYASE / LYTIC TRANSGLYCOSILASE / CELL WALL RECYCLING
Function / homology
Function and homology information


: / peptidoglycan lytic transglycosylase activity / peptidoglycan catabolic process / cell outer membrane / cell wall organization / cell wall macromolecule catabolic process
Similarity search - Function
Membrane-bound lytic murein transglycosylase F / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Membrane-bound lytic murein transglycosylase F / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Lysozyme-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6X4 / : / Membrane-bound lytic murein transglycosylase F / Membrane-bound lytic murein transglycosylase F
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDominguez-Gil, T. / Acebron, I. / Hermoso, J.A.
CitationJournal: Structure / Year: 2016
Title: Activation by Allostery in Cell-Wall Remodeling by a Modular Membrane-Bound Lytic Transglycosylase from Pseudomonas aeruginosa.
Authors: Dominguez-Gil, T. / Lee, M. / Acebron-Avalos, I. / Mahasenan, K.V. / Hesek, D. / Dik, D.A. / Byun, B. / Lastochkin, E. / Fisher, J.F. / Mobashery, S. / Hermoso, J.A.
History
DepositionJul 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / 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 / _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: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
C: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
D: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,0035
Polymers204,5144
Non-polymers4901
Water2,882160
1
A: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6032
Polymers51,1131
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F


Theoretical massNumber of molelcules
Total (without water)51,1431
Polymers51,1431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F


Theoretical massNumber of molelcules
Total (without water)51,1131
Polymers51,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F


Theoretical massNumber of molelcules
Total (without water)51,1431
Polymers51,1431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.116, 136.774, 138.098
Angle α, β, γ (deg.)90.00, 92.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F / MUREIN LYTIC TRANGLYCOSILASE F


Mass: 51113.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: BWHPSA013 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: A0A077JMS0, UniProt: A0A1I9GEN8*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Protein MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F / MUREIN LYTIC TRANGLYCOSILASE F


Mass: 51143.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: BWHPSA013 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: A0A077JMS0, UniProt: A0A1I9GEN9*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#3: Chemical ChemComp-6X4 / [6-[[(2~{R})-1-azanyl-1-oxidanylidene-propan-2-yl]amino]-6-oxidanylidene-5-[[(4~{R})-5-oxidanyl-5-oxidanylidene-4-[[(2~{S})-2-[[(2~{R})-2-oxidanylpropanoyl]amino]propanoyl]amino]pentanoyl]amino]hexyl]azanium


Mass: 489.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H37N6O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST NINE AMINOACIDS FROM ERW72512 SEQUENCE ARE FROM PEPTIDE SIGNAL AND WERE NOT INCLUDED IN OUR CONSTRUCT

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.15 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: ELLIPTICALLY BENT MIRROR
RadiationMonochromator: SI(111) CHANNEL-CUT, CRYOCOOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.72 Å / Num. obs: 94338 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A5X

5a5x


Resolution: 2.4→48.569 Å / SU ML: 0.35 / σ(F): 1.33 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 4680 5 %
Rwork0.1854 --
obs0.1881 94297 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13342 0 34 160 13536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01613655
X-RAY DIFFRACTIONf_angle_d1.59718456
X-RAY DIFFRACTIONf_dihedral_angle_d17.7055139
X-RAY DIFFRACTIONf_chiral_restr0.0821944
X-RAY DIFFRACTIONf_plane_restr0.0082434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.31671740.30563003X-RAY DIFFRACTION100
2.4273-2.45580.32591950.27082971X-RAY DIFFRACTION100
2.4558-2.48580.29641650.26093015X-RAY DIFFRACTION100
2.4858-2.51730.30461740.25512981X-RAY DIFFRACTION100
2.5173-2.55040.3521520.25573060X-RAY DIFFRACTION100
2.5504-2.58530.2881460.25343014X-RAY DIFFRACTION100
2.5853-2.62220.35271410.25433024X-RAY DIFFRACTION100
2.6222-2.66140.31741610.25043026X-RAY DIFFRACTION100
2.6614-2.7030.33481440.25453010X-RAY DIFFRACTION100
2.703-2.74730.32721320.25653059X-RAY DIFFRACTION100
2.7473-2.79460.32551480.26813027X-RAY DIFFRACTION100
2.7946-2.84550.2971580.25323023X-RAY DIFFRACTION100
2.8455-2.90020.3321710.24793003X-RAY DIFFRACTION100
2.9002-2.95940.26281350.23433035X-RAY DIFFRACTION100
2.9594-3.02370.2921270.23143065X-RAY DIFFRACTION100
3.0237-3.0940.29381520.22593039X-RAY DIFFRACTION100
3.094-3.17140.28211820.22653012X-RAY DIFFRACTION100
3.1714-3.25710.27261630.2392987X-RAY DIFFRACTION100
3.2571-3.35290.29961570.23813048X-RAY DIFFRACTION100
3.3529-3.46110.26421190.21993101X-RAY DIFFRACTION100
3.4611-3.58480.28741690.20952964X-RAY DIFFRACTION100
3.5848-3.72830.3129970.19921774X-RAY DIFFRACTION58
3.7283-3.89790.22661220.1823101X-RAY DIFFRACTION100
3.8979-4.10330.20261840.15932982X-RAY DIFFRACTION100
4.1033-4.36020.19761820.15053002X-RAY DIFFRACTION100
4.3602-4.69660.19541730.13453046X-RAY DIFFRACTION100
4.6966-5.16880.21551690.14123029X-RAY DIFFRACTION100
5.1688-5.91560.22591720.153042X-RAY DIFFRACTION100
5.9156-7.44870.2071600.15713063X-RAY DIFFRACTION100
7.4487-48.57920.14291560.11923111X-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