[English] 日本語
Yorodumi
- PDB-4qdn: Crystal Structure of the endo-beta-N-acetylglucosaminidase from T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qdn
TitleCrystal Structure of the endo-beta-N-acetylglucosaminidase from Thermotoga maritima
ComponentsFlagellar protein FlgJ [peptidoglycan hydrolase]
KeywordsHYDROLASE / GH73 family (Cazy database) / inverting mechanism / bacterial peptidoglycan hydrolysis / typical lysozyme alpha-beta fold with only the alpha-lobe / Glycoside hydrolase
Function / homology
Function and homology information


Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / Lysozyme - #10 / Lysozyme / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Flagellar-related protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLipski, A. / Nurizzo, D. / Bourne, Y. / Vincent, F.
CitationJournal: Glycobiology / Year: 2015
Title: Structural and biochemical characterization of the beta-N-acetylglucosaminidase from Thermotoga maritima: Toward rationalization of mechanistic knowledge in the GH73 family.
Authors: Lipski, A. / Herve, M. / Lombard, V. / Nurizzo, D. / Mengin-Lecreulx, D. / Bourne, Y. / Vincent, F.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Flagellar protein FlgJ [peptidoglycan hydrolase]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0593
Polymers15,8461
Non-polymers2132
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Flagellar protein FlgJ [peptidoglycan hydrolase]
hetero molecules

A: Flagellar protein FlgJ [peptidoglycan hydrolase]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1196
Polymers31,6922
Non-polymers4264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3150 Å2
ΔGint-54 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.560, 61.194, 101.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

-
Components

#1: Protein Flagellar protein FlgJ [peptidoglycan hydrolase] / Flagellar-related protein / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase


Mass: 15846.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: THEMA_01495, TM0633, Tmari_0634, TM_0633 / Plasmid: pDEST14-TM0633 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q9WZA1, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50% MPD, 0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2009
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→50.6 Å / Num. all: 16301 / Num. obs: 16057 / % possible obs: 98.6 % / Observed criterion σ(F): 0.08 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.086 / Net I/σ(I): 13.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2119 / % possible all: 91

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→37.054 Å / SU ML: 0.08 / σ(F): 1.35 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 330 2.06 %RANDOM
Rwork0.1669 ---
obs0.1675 16052 98.48 %-
all-16052 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→37.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 13 70 1046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061063
X-RAY DIFFRACTIONf_angle_d0.961447
X-RAY DIFFRACTIONf_dihedral_angle_d15.443418
X-RAY DIFFRACTIONf_chiral_restr0.042155
X-RAY DIFFRACTIONf_plane_restr0.003183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-2.1420.23021630.18597649X-RAY DIFFRACTION97
2.142-37.06310.18351670.16178073X-RAY DIFFRACTION100
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)
12.96731.45320.34072.31593.14015.90730.05850.1102-0.1605-0.1964-0.15110.22290.2422-0.66380.09770.1621-0.0353-0.00810.18510.03480.1493-5.42172.148616.494
24.0004-5.0875-4.49059.42516.27077.75040.00580.12110.1224-0.2470.1437-0.1416-0.15140.0736-0.19060.1783-0.06130.0050.15530.01150.14111.09435.87911.2757
35.6313-1.25616.34824.9855-5.29372.00191.01730.5108-0.4503-1.1191-0.35590.15540.51810.868-0.66790.33420.01550.00490.2856-0.02420.20243.7506-6.15318.526
41.90730.11682.94046.1541-2.40826.435-0.07710.1660.1381-0.39570.1257-0.45050.17650.9385-0.06960.1764-0.00010.03580.306-0.05190.203910.0276-0.188516.8415
57.2251-6.26964.78615.5525-4.83657.19930.20130.46150.1739-0.05030.50620.25820.118-0.0935-0.57530.3868-0.0707-0.12210.8241-0.10841.099619.00438.904119.0571
62.84531.1938-0.61346.1197-2.24824.5967-0.06990.01120.0743-0.06250.1274-0.3643-0.08960.6225-0.0970.0982-0.02220.02070.2276-0.04560.1568.56255.591120.9224
76.8791.49211.38382.0237-1.37813.95080.11080.07141.0112-0.41550.0208-0.012-1.32930.14-0.14730.4366-0.08040.07830.1345-0.01670.3354.138219.711313.0157
88.43821.0826-0.42554.23451.25124.4339-0.09830.88150.1637-0.55020.0633-0.2894-0.53310.54270.01180.2941-0.09540.06510.27350.02020.20258.422513.76454.9849
95.69442.8122-2.97168.2534-2.50492.2827-0.51640.65150.0612-0.96480.52610.334-0.1864-0.2102-0.13280.334-0.0861-0.01940.25380.00930.13610.58916.93012.395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 40 )
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 55 )
6X-RAY DIFFRACTION6chain 'A' and (resid 74 through 95 )
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 105 )
8X-RAY DIFFRACTION8chain 'A' and (resid 106 through 123 )
9X-RAY DIFFRACTION9chain 'A' and (resid 124 through 136 )

+
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://pdbjlvh1.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