[English] 日本語
Yorodumi
- PDB-4hjv: Crystal structure of E. coli MltE with bound bulgecin and murodip... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hjv
TitleCrystal structure of E. coli MltE with bound bulgecin and murodipeptide
ComponentsEndo-type membrane-bound lytic murein transglycosylase A
KeywordsLYASE/LYASE INHIBITOR / goose type lysozyme-like structure / lytic transglycosylase / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


: / lytic endotransglycosylase activity / lytic transglycosylase activity / peptidoglycan metabolic process / cell outer membrane / cell wall organization / cell wall macromolecule catabolic process / cell division
Similarity search - Function
Endo-type membrane-bound lytic murein transglycosylase A / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-BLG / Endo-type membrane-bound lytic murein transglycosylase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFibriansah, G. / Gliubich, F.I. / Thunnissen, A.-M.W.H.
CitationJournal: Biochemistry / Year: 2012
Title: On the Mechanism of Peptidoglycan Binding and Cleavage by the endo-Specific Lytic Transglycosylase MltE from Escherichia coli.
Authors: Fibriansah, G. / Gliubich, F.I. / Thunnissen, A.M.
History
DepositionOct 14, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 24, 2012ID: 3T4I
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / 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_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endo-type membrane-bound lytic murein transglycosylase A
B: Endo-type membrane-bound lytic murein transglycosylase A
C: Endo-type membrane-bound lytic murein transglycosylase A
D: Endo-type membrane-bound lytic murein transglycosylase A
E: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,02915
Polymers111,0415
Non-polymers3,98810
Water8,593477
1
A: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2573
Polymers22,2081
Non-polymers1,0492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8573
Polymers22,2081
Non-polymers6492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3534
Polymers22,2081
Non-polymers1,1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2573
Polymers22,2081
Non-polymers1,0492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Endo-type membrane-bound lytic murein transglycosylase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3042
Polymers22,2081
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.778, 94.853, 162.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Endo-type membrane-bound lytic murein transglycosylase A / Peptidoglycan lytic endotransglycosylase


Mass: 22208.146 Da / Num. of mol.: 5 / Fragment: UNP residues 17-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: emtA, mltE, sltZ, ycgP, b1193, JW5821 / Plasmid: pMT429-emtA / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
References: UniProt: P0C960, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid


Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][<C3O2>]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-BLG / 4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE / BULGECIN A


Mass: 552.551 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H30N3O14S2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M lithium sulfate, 15% PEG8000, 20 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.842 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1998 / Details: mirror
RadiationMonochromator: Si(111), horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.842 Å / Relative weight: 1
ReflectionResolution: 2.3→23 Å / Num. obs: 54621 / % possible obs: 98.2 % / Redundancy: 4.3 % / Rsym value: 0.063 / Net I/σ(I): 13.1

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T36

3t36


Resolution: 2.3→22.758 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 5514 10.12 %
Rwork0.1627 --
obs0.1668 54478 99.7 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→22.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7069 0 257 477 7803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097503
X-RAY DIFFRACTIONf_angle_d1.18510222
X-RAY DIFFRACTIONf_dihedral_angle_d17.2132874
X-RAY DIFFRACTIONf_chiral_restr0.0761137
X-RAY DIFFRACTIONf_plane_restr0.0061311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.24175450.18874789X-RAY DIFFRACTION99
2.3822-2.47750.23645660.17374816X-RAY DIFFRACTION100
2.4775-2.59010.2155650.16034811X-RAY DIFFRACTION100
2.5901-2.72640.21765520.16694880X-RAY DIFFRACTION100
2.7264-2.89690.21525490.16464850X-RAY DIFFRACTION100
2.8969-3.12010.23215450.16984882X-RAY DIFFRACTION100
3.1201-3.43310.21425480.17364924X-RAY DIFFRACTION100
3.4331-3.92770.19335090.1644956X-RAY DIFFRACTION100
3.9277-4.94010.17235420.14235000X-RAY DIFFRACTION100
4.9401-22.75930.18985930.16215056X-RAY DIFFRACTION99
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)
12.8108-0.01120.22552.0208-0.6261.3002-0.0625-0.1006-0.07210.1640.0173-0.1883-0.0195-0.09850.03850.2655-0.003-0.06220.2538-0.05650.209357.018841.324955.6201
21.56410.18410.24952.1087-0.1532.2588-0.0071-0.04780.0912-0.02010.10630.1224-0.0587-0.0934-0.10260.156-0.0072-0.02110.1854-0.01620.232548.031568.424433.9489
31.9341-0.3049-0.63792.5553-0.66053.31640.13660.04570.27480.1001-0.1728-0.1474-0.36720.29070.02330.1711-0.02340.00240.24780.01710.220614.888351.655459.8174
42.2709-0.0951-0.72771.9857-0.13343.2669-0.10720.2702-0.1602-0.0894-0.01820.3295-0.0451-0.26640.11570.27370.0535-0.06140.33180.04420.42278.100555.37424.6002
52.528-0.1524-0.02812.2685-0.08924.4356-0.07480.0131-0.2409-0.1301-0.0366-0.19860.59260.23070.09310.33720.0444-0.00040.21710.01950.212942.256287.698467.8952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 203 )
2X-RAY DIFFRACTION2chain 'B' and (resid 19 through 203 )
3X-RAY DIFFRACTION3chain 'C' and (resid 19 through 203 )
4X-RAY DIFFRACTION4chain 'D' and (resid 22 through 203 )
5X-RAY DIFFRACTION5chain 'E' and (resid 19 through 203 )

+
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