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- PDB-1mu4: CRYSTAL STRUCTURE AT 1.8 ANGSTROMS OF THE BACILLUS SUBTILIS CATAB... -

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Basic information

Entry
Database: PDB / ID: 1mu4
TitleCRYSTAL STRUCTURE AT 1.8 ANGSTROMS OF THE BACILLUS SUBTILIS CATABOLITE REPRESSION HISTIDINE CONTAINING PROTEIN (CRH)
ComponentsHPr-like protein crh
KeywordsTRANSPORT PROTEIN / OPEN-FACED B-SANDWICH / PHOSPHOTRANSFERASE SYSTEM / SWAPPING DOMAIN
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system
Similarity search - Function
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
HPr-like protein Crh
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJuy, M.R. / Haser, R.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Dimerization of Crh by reversible 3D Domain Swapping Induces Structural Adjustments to its monomeric homologue HPR
Authors: Juy, M.R. / Penin, F. / Favier, A. / Galinier, A. / Montserret, R. / Haser, R. / Deutscher, J. / Bockmann, A.
#1: Journal: J.MOL.MICROBIOL.BIOTECHNOL. / Year: 2001
Title: Evidence for a Dimerisation State of the Bacillus Subtilis Catabolite Repression Hpr-Like Protein, Crh
Authors: Penin, F. / Favier, A. / Montserret, R. / Brutscher, B. / Deutscher, J. / Marion, D. / Galinier, D.
History
DepositionSep 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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_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_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

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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)19,4445
Polymers19,1562
Non-polymers2883
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-51 kcal/mol
Surface area9390 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)38,88810
Polymers38,3124
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_756-x+2,y,-z+11
Buried area11430 Å2
ΔGint-130 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.850, 68.850, 119.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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


Mass: 9577.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O06976
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.71 Å3/Da / Density % sol: 66.82 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, peg 1000,, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
32 %(v/v)PEG10001reservoir
420 mM1reservoirpH6.5NH4HCO3
520 mM1dropNH4HCO3

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 8, 2001
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→29.85 Å / Num. all: 27502 / Num. obs: 27502 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 8.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2112 / Rsym value: 0.318 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. obs: 27478
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MO1

1mo1


Resolution: 1.8→29.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1664964.41 / Data cutoff high rms absF: 1664964.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1342 4.9 %RANDOM
Rwork0.179 ---
all0.196 27478 --
obs0.179 27441 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.8 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 15 122 1467
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it2.981.5
X-RAY DIFFRACTIONc_mcangle_it4.022
X-RAY DIFFRACTIONc_scbond_it6.742
X-RAY DIFFRACTIONc_scangle_it9.912.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 218 4.9 %
Rwork0.214 4274 -
obs-4274 100 %
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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