[English] 日本語
Yorodumi
- PDB-1j6w: CRYSTAL STRUCTURE OF HAEMOPHILUS INFLUENZAE LUXS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j6w
TitleCRYSTAL STRUCTURE OF HAEMOPHILUS INFLUENZAE LUXS
ComponentsAUTOINDUCER-2 PRODUCTION PROTEIN LUXS
KeywordsSIGNALING PROTEIN / alpha-beta fold
Function / homology
Function and homology information


S-ribosylhomocysteine lyase / S-ribosylhomocysteine lyase activity / L-methionine salvage from S-adenosylmethionine / quorum sensing / iron ion binding / cytosol
Similarity search - Function
S-ribosylhomocysteinase (LuxS) / S-ribosylhomocysteinase (LuxS) / S-ribosylhomocysteinase (LuxS) superfamily / S-Ribosylhomocysteinase (LuxS) / Metalloenzyme, LuxS/M16 peptidase-like / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
METHIONINE / S-ribosylhomocysteine lyase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLewis, H.A. / Furlong, E.B. / Bergseid, M.G. / Sanderson, W.E. / Buchanan, S.G.
Citation
Journal: Structure / Year: 2001
Title: A structural genomics approach to the study of quorum sensing: crystal structures of three LuxS orthologs.
Authors: Lewis, H.A. / Furlong, E.B. / Laubert, B. / Eroshkina, G.A. / Batiyenko, Y. / Adams, J.M. / Bergseid, M.G. / Marsh, C.D. / Peat, T.S. / Sanderson, W.E. / Sauder, J.M. / Buchanan, S.G.
#1: Journal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionMay 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_ref_seq_dif.details / _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: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS
B: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1286
Polymers39,6992
Non-polymers4294
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-110 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.669, 129.669, 53.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Cell settingtetragonal
Space group name H-MP42212

-
Components

#1: Protein AUTOINDUCER-2 PRODUCTION PROTEIN LUXS / AI-2 SYNTHESIS PROTEIN / CONSERVED HYPOTHETICAL PROTEIN HI049


Mass: 19849.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P44007
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: PEG MME 5000, MES, BME, NaCl, pH 6.25, VAPOR DIFFUSION, HANGING DROP at 285K, temperature 285.0K
Crystal grow
*PLUS
Temperature: 12 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
121 %PEG5000 MME1reservoir
2100 mMBis-Tris1reservoir
330 mMbeta-mercaptoethanol1reservoir
410 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795, 0.9641
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 5, 2000
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.96411
ReflectionResolution: 2.1→32 Å / Num. all: 50926 / Num. obs: 50722 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 24.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.094 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.184

-
Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 5072 10 %Random
Rwork0.213 ---
all0.215 50926 --
obs0.215 50722 --
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 20 57 2569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.008
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

+
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