[English] 日本語
Yorodumi
- PDB-6fcr: The X-ray Structure of Lytic Transglycosylase Slt inactive mutant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fcr
TitleThe X-ray Structure of Lytic Transglycosylase Slt inactive mutant E503Q from Pseudomonas aeruginosa in complex with NAG-NAMtetrapeptide-NAG-anhNAMtetrapeptide
Components
  • ALA-DGL-API-DAL
  • Soluble lytic murein transglycosylase
KeywordsLYASE / Lytic Transglycosylase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space
Similarity search - Function
Lytic transglycosylase, superhelical linker / Soluble lytic murein transglycosylase L domain / Lytic transglycosylase, superhelical linker domain superfamily / Lytic transglycosylase, superhelical U-shaped / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-AH0 / polypeptide(D) / Transglycosylase SLT domain-containing protein / Probable soluble lytic transglycosylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBatuecas, M.T. / Dominguez-Gil, T. / Hermoso, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI104987 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Exolytic and endolytic turnover of peptidoglycan by lytic transglycosylase Slt ofPseudomonas aeruginosa.
Authors: Lee, M. / Batuecas, M.T. / Tomoshige, S. / Dominguez-Gil, T. / Mahasenan, K.V. / Dik, D.A. / Hesek, D. / Millan, C. / Uson, I. / Lastochkin, E. / Hermoso, J.A. / Mobashery, S.
History
DepositionDec 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Soluble lytic murein transglycosylase
F: ALA-DGL-API-DAL
G: ALA-DGL-API-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4007
Polymers71,2743
Non-polymers1,1264
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint30 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.703, 166.703, 55.378
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

-
Protein / Polypeptide(D) / Sugars , 3 types, 4 molecules AFG

#1: Protein Soluble lytic murein transglycosylase


Mass: 70350.688 Da / Num. of mol.: 1 / Mutation: E503Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: slt, AOY09_04369, PAMH19_2049 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A069QJX4, UniProt: Q9HZI6*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Polypeptide(D) ALA-DGL-API-DAL


Mass: 461.466 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 699.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C]/1-2-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 129 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-AH0 / 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID / 1,6-anhydro-N-acetylmuramic acid


Mass: 275.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 80mM Tris pH 8.5, 12% PEG 8000 and 160mM calcium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.75→144.37 Å / Num. obs: 23200 / % possible obs: 99.92 % / Redundancy: 9.7 % / Rpim(I) all: 0.052 / Net I/σ(I): 9.65
Reflection shellResolution: 2.75→2.85 Å / Rpim(I) all: 0.53

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OHU

5ohu


Resolution: 2.75→144.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 31.867 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 1.178 / ESU R Free: 0.334 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24492 1146 4.9 %RANDOM
Rwork0.19111 ---
obs0.19377 22044 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.562 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----1.76 Å2
Refinement stepCycle: 1 / Resolution: 2.75→144.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 138 131 5241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195237
X-RAY DIFFRACTIONr_bond_other_d0.0020.024800
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9757107
X-RAY DIFFRACTIONr_angle_other_deg0.967311062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09822.471263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52315846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.861559
X-RAY DIFFRACTIONr_chiral_restr0.0690.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021184
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5545.7832452
X-RAY DIFFRACTIONr_mcbond_other1.5515.7832450
X-RAY DIFFRACTIONr_mcangle_it2.6378.6713062
X-RAY DIFFRACTIONr_mcangle_other2.6378.6723063
X-RAY DIFFRACTIONr_scbond_it1.5856.0042785
X-RAY DIFFRACTIONr_scbond_other1.5856.0052786
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7758.9174046
X-RAY DIFFRACTIONr_long_range_B_refined4.84367.4436073
X-RAY DIFFRACTIONr_long_range_B_other4.84367.4476074
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 92 -
Rwork0.356 1604 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: 68.2798 Å / Origin y: -12.0916 Å / Origin z: -8.0797 Å
111213212223313233
T0.0121 Å2-0.0039 Å2-0.0146 Å2-0.013 Å20.0077 Å2--0.1521 Å2
L0.1426 °2-0.0582 °2-0.1121 °2-0.5246 °20.0725 °2--0.1068 °2
S-0.0023 Å °0.0063 Å °-0.003 Å °-0.0235 Å °0.023 Å °0.086 Å °-0.0077 Å °0.0069 Å °-0.0207 Å °

+
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