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- PDB-1lih: THREE-DIMENSIONAL STRUCTURES OF THE LIGAND-BINDING DOMAIN OF THE ... -

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Basic information

Entry
Database: PDB / ID: 1lih
TitleTHREE-DIMENSIONAL STRUCTURES OF THE LIGAND-BINDING DOMAIN OF THE BACTERIAL ASPARTATE RECEPTOR WITH AND WITHOUT A LIGAND
ComponentsASPARTATE RECEPTOR
KeywordsCHEMOTAXIS
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane
Similarity search - Function
Aspartate receptor, ligand-binding domain / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / : / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain ...Aspartate receptor, ligand-binding domain / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / : / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1,10-PHENANTHROLINE / Methyl-accepting chemotaxis protein II
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsKim, S.-H. / Scott, W. / Yeh, J.I. / Prive, G.G. / Milburn, M.
Citation
Journal: Science / Year: 1991
Title: Three-dimensional structures of the ligand-binding domain of the bacterial aspartate receptor with and without a ligand.
Authors: Milburn, M.V. / Prive, G.G. / Milligan, D.L. / Scott, W.G. / Yeh, J. / Jancarik, J. / Koshland Jr., D.E. / Kim, S.H.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: The Three-Dimensional Structure of the Ligand-Binding Domain of a Wild-Type Bacterial Chemotaxis Receptor. Structural Comparison to the Cross-Linked Mutant Forms and Conformational Changes Upon Ligand Binding
Authors: Yeh, J.I. / Biemann, H.-P. / Pandit, J. / Koshland, D.E. / Kim, S.-H.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structures of the Ligand-Binding Domain of the Aspartate Receptor from Salmonella Typhimurium
Authors: Scott, W.G. / Milligan, D.L. / Milburn, M.V. / Prive, G.G. / Yeh, J. / Koshland Junior, D.E. / Kim, S.-H.
History
DepositionApr 18, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5522
Polymers18,3711
Non-polymers1801
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.030, 80.030, 155.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: THR 87 - ASP 88 OMEGA = 236.79 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
DetailsTHE FOLLOWING CRYSTALLOGRAPHIC TWO-FOLD OPERATION CAN BE APPLIED TO THE COORDINATES IN THIS ENTRY TO OBTAIN A DIMER. SYMTR1 1 0.000000 0.000000 -1.000000 1.00000 SYMTR2 1 0.000000 -1.000000 0.000000 1.00000 SYMTR3 1 0.166700 0.000000 -1.000000 2.00000

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Components

#1: Protein ASPARTATE RECEPTOR


Mass: 18371.432 Da / Num. of mol.: 1 / Mutation: INS(MET 25), N36C
Source method: isolated from a genetically manipulated source
Details: CYS 36 CROSSLINKED PERIPLASMIC DOMAIN / Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P02941
#2: Chemical ChemComp-PHN / 1,10-PHENANTHROLINE


Mass: 180.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.05 MHEPES1drop
30.75 M1dropLi2SO4
40.5 mMCu(II)[1,10-phenanthroline]31drop
50.1 MHEPES1reservoir
61.5 M1reservoirLi2SO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.188 / Rfactor obs: 0.188 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 14 116 1374
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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