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- PDB-1mo1: CRYSTAL STRUCTURE AT 1.8 ANGSTROMS OF SELENO METHIONYLED CRH, THE... -

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Basic information

Entry
Database: PDB / ID: 1mo1
TitleCRYSTAL STRUCTURE AT 1.8 ANGSTROMS OF SELENO METHIONYLED CRH, THE BACILLUS SUBTILIS CATABOLITE REPRESSION CONTAINING PROTEIN CRH REVEALS AN UNEXPECTED SWAPPING DOMAIN AS AN UNTERTWINNED DIMER
Components(Hpr-like protein crh) x 2
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 / MAD / Resolution: 1.8 Å
AuthorsJuy, M.R. / Haser, R.
Citation
Journal: To be Published
Title: Crystal Structure at 1.8 A of the Bacillus Subtil Catabolite Bacillus Subtilis Catabolite Repression Containing Protein (Crh) Reveals an Unexpected Swapping Domain as an Untertwinned Dimer
Authors: Juy, M.R. / Bockmann, A. / Galinier, A. / Penin, F. / Haser, R.
#1: Journal: J.Mol.Microbiol.Biotechnol. / Year: 2001
Title: Evidence for a Dimerisation State of the Bacillus subtilis Catabolite Repression repression Hpr-like Protein Crh
Authors: Penin, F. / Favier, A. / Montserret, R. / Brutscher, B. / Deutscher, J. / Marion, D. / Galinier, A.
History
DepositionSep 6, 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: Non-polymer description / Version format compliance
Revision 1.3Jul 21, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: refine / reflns ...refine / reflns / reflns_shell / struct_conn / struct_ref_seq_dif / struct_site
Item: _refine.ls_percent_reflns_obs / _reflns.percent_possible_obs ..._refine.ls_percent_reflns_obs / _reflns.percent_possible_obs / _reflns_shell.percent_possible_all / _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
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Hpr-like protein crh
B: Hpr-like protein crh
C: Hpr-like protein crh
D: Hpr-like protein crh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,57023
Polymers38,7814
Non-polymers1,78919
Water8,467470
1
A: Hpr-like protein crh
B: Hpr-like protein crh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,33512
Polymers19,3902
Non-polymers94510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-72 kcal/mol
Surface area9670 Å2
MethodPISA
2
C: Hpr-like protein crh
D: Hpr-like protein crh
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,23511
Polymers19,3902
Non-polymers8459
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-73 kcal/mol
Surface area9640 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14390 Å2
ΔGint-181 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.240, 68.240, 115.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 9671.743 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: Protein Hpr-like protein crh / Catabolite repression HPr


Mass: 9718.639 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.79 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, PEG 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763,0.9798,0.9801
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 8, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
20.97981
30.98011
ReflectionResolution: 1.8→24.75 Å / Num. all: 48746 / Num. obs: 46777 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.028 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 3.6 / Num. unique all: 7247 / Rsym value: 0.15 / % possible all: 94

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→24.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1471610.97 / Data cutoff high rms absF: 1471610.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2370 5.1 %RANDOM
Rwork0.164 ---
all-46777 --
obs-44407 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9955 Å2 / ksol: 0.379036 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 104 470 3254
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.29
X-RAY DIFFRACTIONc_mcbond_it2.771.5
X-RAY DIFFRACTIONc_mcangle_it3.452
X-RAY DIFFRACTIONc_scbond_it5.912
X-RAY DIFFRACTIONc_scangle_it7.722.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 402 5.3 %
Rwork0.182 7247 -
obs-7247 94.7 %

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