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- PDB-1vlt: LIGAND BINDING DOMAIN OF THE WILD-TYPE ASPARTATE RECEPTOR WITH AS... -

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Basic information

Entry
Database: PDB / ID: 1vlt
TitleLIGAND BINDING DOMAIN OF THE WILD-TYPE ASPARTATE RECEPTOR WITH ASPARTATE
ComponentsASPARTATE RECEPTOR
KeywordsCOMPLEX (CHEMOTAXIS/PEPTIDE) / COMPLEX (CHEMOTAXIS-PEPTIDE) / CHEMOTAXIS / BACTERIAL CHEMOTAXIS RECEPTOR / BOUND / COMPLEX (CHEMOTAXIS-PEPTIDE) complex
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
ASPARTIC ACID / Methyl-accepting chemotaxis protein II
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 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 1.0May 15, 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 ...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_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_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

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE RECEPTOR
B: ASPARTATE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9994
Polymers32,7322
Non-polymers2662
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.670, 72.740, 73.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ASPARTATE RECEPTOR / TAR


Mass: 16366.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P02941
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.47 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 M1reservoirCdCl2
20.1 Macetate1reservoir
340 %PEG4001reservoir
40.05 M1dropCdCl2
50.05 Macetate1drop
620 %PEG4001drop
75 mMaspartate1drop

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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: 3.5 % / Rmerge(I) obs: 0.079
Reflection
*PLUS
Highest resolution: 2.19 Å / Lowest resolution: 6 Å / Num. obs: 15964 / Num. measured all: 56261

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Processing

Software
NameVersionClassification
MSCSOFTWAREdata collection
X-PLORmodel building
X-PLORrefinement
MSCdata reduction
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.198 --
obs0.198 15964 93 %
Displacement parametersBiso mean: 33.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 0 160 2389
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.76
X-RAY DIFFRACTIONx_dihedral_angle_deg20.9

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