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- PDB-1wat: THE THREE-DIMENSIONAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF A... -

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Basic information

Entry
Database: PDB / ID: 1wat
TitleTHE THREE-DIMENSIONAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF A WILD-TYPE BACTERIAL CHEMOTAXIS RECEPTOR
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
ASPARTIC ACID / Methyl-accepting chemotaxis protein II
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsKim, S.-H.
Citation
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.
#1: 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.I. / Jancarik, J. / Koshland Junior, D.E. / Kim, S.-H.
History
DepositionMar 9, 1993Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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)32,8663
Polymers32,7322
Non-polymers1331
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.670, 132.670, 55.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: THR A 111 - PRO A 112 OMEGA = 111.59 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: LEU A 113 - PRO A 114 OMEGA = 211.53 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: THR B 179 - PHE B 180 OMEGA = 84.24 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: THE LOOP REGIONS, RESIDUES A 76 - A 84 AND B 76 - B 84, ARE DISORDERED.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8583, 0.439267, 0.2652), (0.40534, 0.263599, 0.8753), (0.3146, 0.858813, -0.404)
Vector: 281.17169, 44.93618, -203.22099)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL GENERATE APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THIS CORRESPONDS TO A ROTATION OF 178.2 DEGREES, WHICH IS AN APPROXIMATE (MOLECULAR) TWO-FOLD.

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Components

#1: Protein ASPARTATE RECEPTOR


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.: 1 / Source method: obtained synthetically / Formula: C4H7NO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.34 Å3/Da / Density % sol: 71.68 %
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Mammonium sulfate1reservoir
235 %PEG80001reservoir
325 mMasparatate 1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 7114 / % possible obs: 62 % / Num. measured all: 15061 / Rmerge(I) obs: 0.071

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 3 Å / σ(F): 1.5
Details: THE LOOP REGIONS, RESIDUES A 76 - A 84 AND B 76 - B 84, ARE DISORDERED.
RfactorNum. reflection
Rwork0.192 -
obs0.192 7114
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 0 0 2238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.696
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.5 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.696

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