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- PDB-1hpb: THE BACTERIAL PERIPLASMIC HISTIDINE-BINDING PROTEIN: STRUCTURE(SL... -

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Basic information

Entry
Database: PDB / ID: 1hpb
TitleTHE BACTERIAL PERIPLASMIC HISTIDINE-BINDING PROTEIN: STRUCTURE(SLASH)FUNCTION ANALYSIS OF THE LIGAND-BINDING SITE AND COMPARISON WITH RELATED PROTEINS
ComponentsHISTIDINE-BINDING PROTEIN
KeywordsHISTIDINE-BINDING PROTEIN
Function / homology
Function and homology information


amino acid transport / outer membrane-bounded periplasmic space
Similarity search - Function
Specific amino acids and opine-binding periplasmic protein, ABC transporter / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF
Similarity search - Domain/homology
HISTIDINE / Histidine-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsKim, S.H. / Oh, B.H.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: The bacterial periplasmic histidine-binding protein. structure/function analysis of the ligand-binding site and comparison with related proteins.
Authors: Oh, B.H. / Kang, C.H. / De Bondt, H. / Kim, S.H. / Nikaido, K. / Joshi, A.K. / Ames, G.F.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Three-Dimensional Structures of the Periplasmic Lysine-, Arginine-, Ornithine-Binding Protein with and without a Ligand
Authors: Oh, B.-H. / Pandit, J. / Kang, C.-H. / Nikaido, K. / Gokcen, S. / Ames, G.F. / Kim, S.-H.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Crystal Structure of the Lysine-, Arginine-, Ornithine-Binding Protein from Salmonella Typhimurium at 2.7 Angstroms Resolution
Authors: Kang, C.-H. / Shin, W.-C. / Yamagata, Y. / Gokcen, S. / Ames, G.F.-L. / Kim, S.-H.
History
DepositionSep 30, 1993Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
P: HISTIDINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3462
Polymers26,1901
Non-polymers1561
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.260, 66.170, 88.130
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 HISTIDINE-BINDING PROTEIN / Coordinate model: Cα atoms only


Mass: 26189.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P02910
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.3 M1reservoirMgCl2
30.1 MTris-HCl1reservoir
425 %PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 6525 / % possible obs: 77.2 % / Rmerge(I) obs: 0.0821

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.192 / Rfactor obs: 0.192 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms238 0 11 0 249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg3.64
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
Lowest resolution: 6 Å / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.64
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_deg1.6

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