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- PDB-2ak7: structure of a dimeric P-Ser-Crh -

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Basic information

Entry
Database: PDB / ID: 2ak7
Titlestructure of a dimeric P-Ser-Crh
ComponentsHPr-like protein crh
KeywordsTRANSPORT PROTEIN / Crh / P-Crh
Function / homology
Function and homology information


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
HPr-like protein Crh
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChaptal, V. / Gueguen-Chaignon, V. / Poncet, S. / Lecampion, C. / Lariviere, L. / Meyer, P. / Galinier, A. / Deutscher, J. / Nessler, S. / Morera, S.
CitationJournal: Proteins / Year: 2006
Title: X-ray structure of a domain-swapped dimer of Ser46-phosphorylated Crh from Bacillus subtilis.
Authors: Chaptal, V. / Lariviere, L. / Gueguen-Chaignon, V. / Galinier, A. / Nessler, S. / Morera, S.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: HPr-like protein crh
B: HPr-like protein crh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2524
Polymers19,0602
Non-polymers1922
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-44 kcal/mol
Surface area9140 Å2
MethodPISA
2
A: HPr-like protein crh
B: HPr-like protein crh
hetero molecules

A: HPr-like protein crh
B: HPr-like protein crh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5038
Polymers38,1194
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_656-x+1,y,-z+11
Buried area11290 Å2
ΔGint-114 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.697, 67.697, 117.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
DetailsThe biological assembly is a dimer in the asymetric unit.

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Components

#1: Protein HPr-like protein crh / Catabolite repression HPr


Mass: 9529.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: crh / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O06976
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2004
RadiationMonochromator: 0.98 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 19078 / Num. obs: 19067 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 22.05 Å2 / Rsym value: 0.082 / Net I/σ(I): 4.8
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2 / Num. unique all: 1850 / Rsym value: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MU4

1mu4


Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.214 929 random
Rwork0.199 --
all-19078 -
obs-19067 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 10 169 1509
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_angle_d1.22

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