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- PDB-3lfg: Crystal structure of HPr-C-His from Thermoanaerobacter tengcongensis -

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Basic information

Entry
Database: PDB / ID: 3lfg
TitleCrystal structure of HPr-C-His from Thermoanaerobacter tengcongensis
ComponentsPhosphotransferase system, HPr-related proteinsPEP group translocation
KeywordsTRANSFERASE / HPr fruB phosphotransfer PTS / 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: 1.58 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 17, 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 ...chem_comp_atom / chem_comp_bond / database_2 / 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
C: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)32,0743
Polymers32,0743
Non-polymers00
Water4,954275
1
A: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)10,6911
Polymers10,6911
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)10,6911
Polymers10,6911
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)10,6911
Polymers10,6911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.712, 68.841, 78.170
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 / PEP group translocation


Mass: 10691.167 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 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 4000, 0.1M NaAc pH 4.6, 0.2M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 37529 / Num. obs: 37192 / % possible obs: 99.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.36 Å2 / Rsym value: 0.116
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 4.7 % / Num. unique all: 1683 / % possible all: 91.4

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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 / Resolution: 1.58→28.16 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.863 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 1695 5.07 %
Rwork0.1905 --
obs0.1917 33413 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.793 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 62.92 Å2 / Biso mean: 19.972 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1--2.993 Å2-0 Å20 Å2
2---5.646 Å2-0 Å2
3---8.639 Å2
Refinement stepCycle: LAST / Resolution: 1.58→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 0 275 2224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091977
X-RAY DIFFRACTIONf_angle_d1.1092661
X-RAY DIFFRACTIONf_chiral_restr0.284324
X-RAY DIFFRACTIONf_plane_restr0.005334
X-RAY DIFFRACTIONf_dihedral_angle_d12.994722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.6260.2341320.1729633095100
1.626-1.6790.2021550.16229473102100
1.679-1.7390.21870.15229133100100
1.739-1.8090.191460.15529803126100
1.809-1.8910.1881210.1732663278497
1.891-1.990.22900.2041623171369
1.99-2.1150.1771600.1729673127100
2.115-2.2780.23980.1721701179997
2.278-2.5070.1981420.1842792293499
2.507-2.870.2141620.18729983160100
2.87-3.6150.1991640.192745290998
3.615-28.1640.21380.1862426256484
Refinement TLS params.Method: refined / Origin x: 11.16 Å / Origin y: -10.8294 Å / Origin z: 11.0281 Å
111213212223313233
T0.1036 Å2-0.0018 Å2-0.009 Å2-0.104 Å2-0.0109 Å2--0.0946 Å2
L0.1656 °2-0.0628 °2-0.0582 °2-0.3064 °2-0.2154 °2--0.2341 °2
S0.0125 Å °0.0009 Å °0.0128 Å °-0.0155 Å °-0.0093 Å °-0.0094 Å °0.0059 Å °0.0047 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 88
2X-RAY DIFFRACTION1allB1 - 89
3X-RAY DIFFRACTION1allC1 - 88
4X-RAY DIFFRACTION1allB1 - 277

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