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- PDB-1vls: LIGAND BINDING DOMAIN OF THE WILD-TYPE ASPARTATE RECEPTOR -

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Basic information

Entry
Database: PDB / ID: 1vls
TitleLIGAND BINDING DOMAIN OF THE WILD-TYPE ASPARTATE RECEPTOR
ComponentsASPARTATE RECEPTORMethyl-accepting chemotaxis proteins
KeywordsCHEMOTAXIS / BACTERIAL CHEMOTAXIS RECEPTOR / UNBOUND
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 / 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
Methyl-accepting chemotaxis protein II
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsKim, S.-H. / Yeh, J.I. / Biemann, H.-P. / Prive, G. / Pandit, J. / Koshland Junior, D.E.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: High-resolution structures of the ligand binding domain of the wild-type bacterial aspartate receptor.
Authors: Yeh, J.I. / Biemann, H.P. / Prive, G.G. / Pandit, 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: 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 Junior, D.E. / Kim, S.H.
History
DepositionSep 17, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)16,3661
Polymers16,3661
Non-polymers00
Water3,945219
1
A: ASPARTATE RECEPTOR

A: ASPARTATE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)32,7322
Polymers32,7322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)65.020, 65.020, 72.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein ASPARTATE RECEPTOR / Methyl-accepting chemotaxis proteins / TAR


Mass: 16366.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P02941
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.34 Å3/Da / Density % sol: 42 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 M1reservoirCdSO4
20.1 MHEPES1reservoir
31.0 MNa acetate1reservoir
40.05 M1dropCdSO4
50.5 MHEPES1drop
60.50 MNa acetate1drop
710 mg/mlprotein1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 4.2 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 6 Å / Num. obs: 12189 / Num. measured all: 51445

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MSCdata reduction
X-PLORphasing
RefinementResolution: 1.85→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.197 --
obs0.197 12189 98 %
Displacement parametersBiso mean: 32.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 0 190 1334
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4

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