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- PDB-1sph: REFINED STRUCTURES OF THE ACTIVE S83C AND IMPAIRED S46D HPRS: EVI... -

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Basic information

Entry
Database: PDB / ID: 1sph
TitleREFINED STRUCTURES OF THE ACTIVE S83C AND IMPAIRED S46D HPRS: EVIDENCE THAT PHOSPHORYLATION DOES NOT REQUIRE A BACKBONE CONFORMATIONAL TRANSITION
ComponentsHISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


regulation of carbohydrate utilization / phosphoenolpyruvate-dependent sugar phosphotransferase system / cytoplasm
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLiao, D.-I. / Herzberg, O.
Citation
Journal: Structure / Year: 1994
Title: Refined structures of the active Ser83-->Cys and impaired Ser46-->Asp histidine-containing phosphocarrier proteins.
Authors: Liao, D.I. / Herzberg, O.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Structure of the Histidine-Containing Phosphocarrier Protein Hpr from Bacillus Subtilis at 2.0-Angstroms Resolution
Authors: Herzberg, O. / Reddy, P. / Sutrina, S. / Saier Junior, M.H. / Reizer, J. / Kapadia, G.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization of the Bacillus Subtilis Histidine-Containing Phosphocarrier Protein Hpr and Some of its Site-Directed Mutants
Authors: Kapadia, G. / Reizer, J. / Sutrina, S. / Saier Junior, M.H. / Reddy, P. / Herzberg, O.
History
DepositionNov 3, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR
B: HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR


Theoretical massNumber of molelcules
Total (without water)18,4532
Polymers18,4532
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.500, 25.700, 60.400
Angle α, β, γ (deg.)90.00, 108.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.67413, -0.02956, -0.73802), (0.04552, -0.99896, -0.00158), (-0.73721, -0.03466, 0.67477)
Vector: 45.94, 3.92, 20.11)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO CHAIN A WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES RMSD M1 A 2 - A 88 B 2 - B 88 0.29

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Components

#1: Protein HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR


Mass: 9226.345 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: PTSH / Plasmid: PRE GENE: PTSH / References: UniProt: P08877
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.97 Å3/Da / Density % sol: 37.55 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Kapadia, G., (1990) J.Mol.Biol., 212, 1. / PH range low: 5.4 / PH range high: 5.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
174-77 %satammonium salfate1reservoir
20.5-1.5 %(v/v)PEG4001reservoir
3100 mMcitrate1reservoir
410 mg/mlprotein1drop
5reservoir1drop

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Data collection

ReflectionNum. obs: 9111 / % possible obs: 92 % / Observed criterion σ(I): 0
Reflection
*PLUS

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.143 -
obs0.143 7710
Displacement parametersBiso mean: 21.6 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 0 114 1384
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_deg
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: 0.143 / Rfactor Rwork: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg33.64
X-RAY DIFFRACTIONx_plane_restr0.020.016

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