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- PDB-3le5: Crystal structure of HPr dimer from Thermoanaerobacter tengcongensis -

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Basic information

Entry
Database: PDB / ID: 3le5
TitleCrystal structure of HPr dimer from Thermoanaerobacter tengcongensis
ComponentsPhosphotransferase system, HPr-related proteins
KeywordsTRANSFERASE / PTS HPr phosphotransfer / Kinase / Phosphotransferase system
Function / homology
Function and homology information


Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine 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
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)21,3822
Polymers21,3822
Non-polymers00
Water1,69394
1
A: Phosphotransferase system, HPr-related proteins

A: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)21,3822
Polymers21,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area4210 Å2
ΔGint-33 kcal/mol
Surface area8430 Å2
MethodPISA
2
B: Phosphotransferase system, HPr-related proteins

B: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)21,3822
Polymers21,3822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area4460 Å2
ΔGint-40 kcal/mol
Surface area8280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.090, 76.090, 92.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-161-

HOH

21B-97-

HOH

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Components

#1: Protein Phosphotransferase system, HPr-related proteins


Mass: 10691.167 Da / Num. of mol.: 2
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.: 94 / 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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M MgCl2, 0.1M HEPES pH7.5, 30% PEG MME550, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
Reflection twinOperator: -h,k,-l / Fraction: 0.507
ReflectionResolution: 2→50 Å / Num. all: 17800 / Num. obs: 17747 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rsym value: 0.045
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.4 % / Num. unique all: 1762 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MU4

1mu4


Resolution: 2→38.045 Å / σ(F): 1.34 / Phase error: 34.33 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2536 900 5.08 %
Rwork0.2151 --
obs0.2171 17720 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 109.64 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 55.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.068 Å20 Å2-0 Å2
2--0.068 Å20 Å2
3----0.135 Å2
Refinement stepCycle: LAST / Resolution: 2→38.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 0 94 1384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111302
X-RAY DIFFRACTIONf_angle_d0.9311749
X-RAY DIFFRACTIONf_dihedral_angle_d16.133475
X-RAY DIFFRACTIONf_chiral_restr0.064208
X-RAY DIFFRACTIONf_plane_restr0.006223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.08030.3537930.35941892X-RAY DIFFRACTION98
2.0803-2.1750.40261070.35771841X-RAY DIFFRACTION98
2.175-2.28960.3132930.3611884X-RAY DIFFRACTION98
2.2896-2.43310.3918930.37811884X-RAY DIFFRACTION98
2.4331-2.62090.45781170.34571852X-RAY DIFFRACTION98
2.6209-2.88450.431990.33371840X-RAY DIFFRACTION98
2.8845-3.30170.27241010.25771890X-RAY DIFFRACTION98
3.3017-4.1590.1772980.16431883X-RAY DIFFRACTION98
4.159-38.05190.184980.12811855X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 31.4182 Å / Origin y: 18.9745 Å / Origin z: 22.5664 Å
111213212223313233
T0.3889 Å20.0104 Å2-0.0069 Å2-0.3729 Å2-0.0156 Å2--0.3879 Å2
L0.0632 °2-0.0086 °2-0.0286 °2-0.0563 °2-0.2299 °2--0.0323 °2
S0.0605 Å °0.0003 Å °-0.0155 Å °-0.0168 Å °-0.0146 Å °0.0327 Å °-0.0238 Å °0.0984 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 87
2X-RAY DIFFRACTION1allB1 - 87
3X-RAY DIFFRACTION1allA97 - 164
4X-RAY DIFFRACTION1allB97 - 144

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