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- PDB-3le3: Crystal structure of apoHPr monomer from Thermoanaerobacter tengc... -

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Basic information

Entry
Database: PDB / ID: 3le3
TitleCrystal structure of apoHPr monomer from Thermoanaerobacter tengcongensis
ComponentsPhosphotransferase system, HPr-related proteins
KeywordsTRANSFERASE / HPr PTS phosphotransferase / Kinase / Phosphotransferase system
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. / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.861 Å
AuthorsFu, T.M. / Su, X.D.
CitationJournal: To be Published
Title: Dimerization of HPr by reversible domain swapping
Authors: Fu, T.M. / Su, X.D.
History
DepositionJan 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: 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: Phosphotransferase system, HPr-related proteins
B: Phosphotransferase system, HPr-related proteins
C: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)28,8603
Polymers28,8603
Non-polymers00
Water4,954275
1
A: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)9,6201
Polymers9,6201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)9,6201
Polymers9,6201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)9,6201
Polymers9,6201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.296, 70.599, 76.726
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 Phosphotransferase system, HPr-related proteins


Mass: 9620.015 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4T / Gene: FruB, TTE1820 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R910
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M MgCl2, 0.1M HEPES pH7.5, 30% PEG MME 550, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9797 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 23136 / Num. obs: 22049 / % possible obs: 95.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.98 Å2 / Rsym value: 0.034
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 5.8 % / Num. unique all: 1045 / % possible all: 91.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.861→30.275 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1116 5.07 %
Rwork0.1928 --
obs0.1949 21995 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.562 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 21.922 Å2
Baniso -1Baniso -2Baniso -3
1-0.258 Å2-0 Å20 Å2
2---3.849 Å2-0 Å2
3---3.591 Å2
Refinement stepCycle: LAST / Resolution: 1.861→30.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 0 275 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072004
X-RAY DIFFRACTIONf_angle_d0.9192691
X-RAY DIFFRACTIONf_dihedral_angle_d13.899752
X-RAY DIFFRACTIONf_chiral_restr0.062320
X-RAY DIFFRACTIONf_plane_restr0.004340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8607-1.94530.25441350.20322435X-RAY DIFFRACTION91
1.9453-2.04790.22511160.18022485X-RAY DIFFRACTION91
2.0479-2.17610.22841250.17612452X-RAY DIFFRACTION91
2.1761-2.34410.23131360.18892503X-RAY DIFFRACTION92
2.3441-2.57990.23861560.20482604X-RAY DIFFRACTION97
2.5799-2.95290.27731470.2122733X-RAY DIFFRACTION100
2.9529-3.71930.24081670.19572750X-RAY DIFFRACTION100
3.7193-30.27950.19381340.17062917X-RAY DIFFRACTION100

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