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- PDB-1pch: STRUCTURAL EVIDENCE FOR THE EVOLUTIONARY DIVERGENCE OF MYCOPLASMA... -

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Basic information

Entry
Database: PDB / ID: 1pch
TitleSTRUCTURAL EVIDENCE FOR THE EVOLUTIONARY DIVERGENCE OF MYCOPLASMA FROM GRAM-POSITIVE BACTERIA: THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN
ComponentsPHOSPHOCARRIER PROTEIN
KeywordsPHOSPHOTRANSFERASE
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 / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / PTS HPR domain serine phosphorylation site signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesMycoplasma capricolum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsPieper, U. / Herzberg, O.
Citation
Journal: Structure / Year: 1995
Title: Structural evidence for the evolutionary divergence of mycoplasma from gram-positive bacteria: the histidine-containing phosphocarrier protein.
Authors: Pieper, U. / Kapadia, G. / Zhu, P.P. / Peterkofsky, A. / Herzberg, O.
#1: 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.
#2: 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.
History
DepositionJul 11, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 ..._pdbx_database_status.process_site / _software.classification / _software.name / _software.version
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 14, 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
A: PHOSPHOCARRIER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3932
Polymers9,2971
Non-polymers961
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.200, 42.200, 52.400
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 PHOSPHOCARRIER PROTEIN / HPR / HISTIDINE-CONTAINING PROTEIN


Mass: 9296.718 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma capricolum (bacteria) / Gene: PTSH / Plasmid: PRE1 / Gene (production host): PTSH / Production host: Escherichia coli (E. coli) / References: UniProt: P45611
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET 1 WAS PROCESSED DURING THE EXPRESSION IN E. COLI.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.75 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 %satammonium salfate1reservoir
20.1 %(v/v)PEG30001reservoir
3100 mMHEPES1reservoir
410 mg/mlprotein1drop
510 mMTris1drop

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 17, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 6562 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.045
Reflection
*PLUS
Num. all: 7044 / Num. measured all: 18520 / Rmerge(I) obs: 0.045

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Processing

Software
NameVersionClassification
SHELXL-93model building
X-PLOR3.1model building
SHELXL-93refinement
X-PLOR3.1refinement
XENGENdata reduction
SHELXL-93phasing
X-PLOR3.1phasing
RefinementResolution: 1.8→15 Å / σ(F): 0
Details: TWO ALTERNATE CONFORMATIONS HAVE BEEN REFINED FOR THE SIDE CHAIN OF MET 51 WITH OCCUPANCIES OF 0.6 AND 0.4, RESPECTIVELY.
RfactorNum. reflection% reflection
Rwork0.17 --
obs0.17 6562 94 %
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms647 0 5 60 712
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_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.5
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.5

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