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- PDB-1y50: X-ray crystal structure of Bacillus stearothermophilus Histidine ... -

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Basic information

Entry
Database: PDB / ID: 1y50
TitleX-ray crystal structure of Bacillus stearothermophilus Histidine phosphocarrier protein (Hpr) F29W mutant domain_swapped dimer
ComponentsPhosphocarrier protein HPr
KeywordsTRANSPORT PROTEIN / Bacillus stearothermophilus F29W mutant domain-swapped dimer
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. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine 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. ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine 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 speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSridharan, S. / Razvi, A. / Scholtz, J.M. / Sacchettini, J.C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The HPr proteins from the thermophile Bacillus stearothermophilus can form domain-swapped dimers.
Authors: Sridharan, S. / Razvi, A. / Scholtz, J.M. / Sacchettini, J.C.
History
DepositionDec 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5044
Polymers9,2161
Non-polymers2883
Water1,31573
1
A: Phosphocarrier protein HPr
hetero molecules

A: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0088
Polymers18,4312
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area7860 Å2
ΔGint-108 kcal/mol
Surface area8630 Å2
MethodPISA
2
A: Phosphocarrier protein HPr
hetero molecules

A: Phosphocarrier protein HPr
hetero molecules

A: Phosphocarrier protein HPr
hetero molecules

A: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,01516
Polymers36,8624
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area18200 Å2
ΔGint-247 kcal/mol
Surface area14780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)34.861, 63.454, 82.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Phosphocarrier protein HPr / Histidine-containing protein / histidine phosphocarrier protein


Mass: 9215.599 Da / Num. of mol.: 1 / Mutation: F29W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: ptsH / Production host: Escherichia coli (E. coli) / Strain (production host): ES7R / References: UniProt: P42013
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 68-74 % ammonium sulfate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 6544 / Num. obs: 6174 / % possible obs: 94.4 % / Redundancy: 5.2 % / Rsym value: 0.052 / Net I/σ(I): 31.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 456 / Rsym value: 0.244 / % possible all: 70.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wild-type BstHpr

Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.918 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29786 290 4.7 %RANDOM
Rwork0.21518 ---
obs0.21931 5866 94.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.916 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2--1.84 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms635 0 15 73 723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022663
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.993895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.271586
X-RAY DIFFRACTIONr_chiral_restr0.0860.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02457
X-RAY DIFFRACTIONr_nbd_refined0.220.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.214
X-RAY DIFFRACTIONr_mcbond_it2.6175431
X-RAY DIFFRACTIONr_mcangle_it3.8627688
X-RAY DIFFRACTIONr_scbond_it5.5219232
X-RAY DIFFRACTIONr_scangle_it7.56111207
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 10
Rwork0.284 317

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