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- PDB-1qr5: SOLUTION STRUCTURE OF HISTIDINE CONTAINING PROTEIN (HPR) FROM STA... -

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Basic information

Entry
Database: PDB / ID: 1qr5
TitleSOLUTION STRUCTURE OF HISTIDINE CONTAINING PROTEIN (HPR) FROM STAPHYLOCOCCUS CARNOSUS
ComponentsPHOSPHOCARRIER PROTEIN HPR
KeywordsSIGNALING PROTEIN / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


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 speciesStaphylococcus carnosus (bacteria)
MethodSOLUTION NMR / RESTRAINED MD
AuthorsKalbitzer, H.R. / Gorler, A. / Li, H. / Dubovskii, P.V. / Hengstenberg, W. / Kowolik, C. / Yamada, H. / Akasaka, K.
Citation
Journal: Protein Sci. / Year: 2000
Title: 15N and 1H NMR study of histidine containing protein (HPr) from Staphylococcus carnosus at high pressure.
Authors: Kalbitzer, H.R. / Gorler, A. / Li, H. / Dubovskii, P.V. / Hengstenberg, W. / Kowolik, C. / Yamada, H. / Akasaka, K.
#1: Journal: Appl.Magn.Reson. / Year: 1999
Title: Solution Structure of the Histidine-Containing Phosphocarrier Protein from Staphylococcus Aureus
Authors: Gorler, A. / Hengstenberg, W. / Kravanja, M. / Beneicke, W. / Maurer, T. / Kalbitzer, H.R.
History
DepositionMay 19, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list ...pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOCARRIER PROTEIN HPR


Theoretical massNumber of molelcules
Total (without water)9,5191
Polymers9,5191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 2300LOWEST CONFORMATIONAL ENERGY
RepresentativeModel #1

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Components

#1: Protein PHOSPHOCARRIER PROTEIN HPR / HISTIDINE-CONTAINING PROTEIN / HPR


Mass: 9518.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus carnosus (bacteria) / Plasmid: PT7-5 / Production host: Escherichia coli (E. coli) / References: UniProt: P23534

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
141NOESY-HSQC
151TOCSY-HSQC
16115N-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 15N-LABELED PROTEIN.

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Sample preparation

DetailsContents: 90% H2O/10 % D2O
Sample conditionspH: 7.14 / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX 500BrukerAMX 5005001
Bruker DMX 800BrukerDMX 8008002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.51BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: RESTRAINED MD / Software ordinal: 1
Details: RESTRAINED SIMULATED ANEALING PROTOCOL. CONSTRAINTS: 1301 NOES, 523 INTRARESIDUAL (I,I), 382 INTERMEDIATE RANGE (I,I+2), 56 INTERMEDIATE RANGE (I,I+3), 31 INTERMEDIATE RANGE (I,I+4), 224 ...Details: RESTRAINED SIMULATED ANEALING PROTOCOL. CONSTRAINTS: 1301 NOES, 523 INTRARESIDUAL (I,I), 382 INTERMEDIATE RANGE (I,I+2), 56 INTERMEDIATE RANGE (I,I+3), 31 INTERMEDIATE RANGE (I,I+4), 224 LONG RANGE (I,J; J > I+4), 78 J-COUPLINGS (3JNH-HA). STRUCTURAL STATISTICS FOR THE 30 LOWEST-ENERGY STRUCTURES (REFERENCE 1): ENERGIES: TOTAL, 190.8 +-8.4 KJ/MOL; NOE, 57.6 +- 4.6 KJ/MOL; DIHEDRAL, 35.6 +- 6.1 KJ/MOL; BOND, 8.4 +- 0.4 KJ/MOL; ANGLE, 64.0 +-2.6 KJ/MOL; VDW, 16.7 +- 2.3 KJ/MOL; IMPROPER, 8.6 +- 1.2 KJ/MOL; ELECTRIC, 35.6 +- 6.1 kJ/MOL. RMSDS: AMINO ACID 1-88 (WHOLE PROTEIN), BACKBONE ATOMS 0.093 NM, ALL NON-HYDROGEN ATOMS 0.13 NM. RMSDS: AMINO ACID 8-19 (ACTIVE CENTER), BACKBONE ATOMS 0.091 NM, ALL NON-HYDROGEN ATOMS 0.13 NM.
NMR ensembleConformer selection criteria: LOWEST CONFORMATIONAL ENERGY / Conformers calculated total number: 2300 / Conformers submitted total number: 10

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