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- PDB-3bjv: The Crystal Structure of a putative PTS IIA(PtxA) from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 3bjv
TitleThe Crystal Structure of a putative PTS IIA(PtxA) from Streptococcus mutans
ComponentsRmpA
KeywordsTRANSFERASE / alpha/beta three layer sandwich
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm
Similarity search - Function
: / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Phosphotransferase/anion transporter / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ascorbate-specific PTS system EIIA component
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsLei, J. / Liang, Y.H. / Su, X.D.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of phosphotransferase system enzymes PtxB (IIB(Asc)) and PtxA (IIA(Asc)) from Streptococcus mutans
Authors: Lei, J. / Li, L.-F. / Su, X.-D.
History
DepositionDec 4, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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
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: RmpA


Theoretical massNumber of molelcules
Total (without water)17,6961
Polymers17,6961
Non-polymers00
Water81145
1
A: RmpA

A: RmpA


Theoretical massNumber of molelcules
Total (without water)35,3922
Polymers35,3922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area1970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.754, 40.754, 169.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RmpA / Putative PTS system / enzyme IIA component


Mass: 17696.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: ptxA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q93DA9, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.9
Details: 0.1M Tris-Hcl, 1.9-2.1M (NH4)2SO4, pH 7.9, Vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 2, 2007
RadiationMonochromator: multilayer mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40.65 Å / Num. all: 6206 / Num. obs: 6026 / % possible obs: 97.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.0717 / Rsym value: 0.0717 / Net I/σ(I): 10.08
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 9 % / Rmerge(I) obs: 0.1297 / Mean I/σ(I) obs: 0.1297 / Num. unique all: 897 / Rsym value: 0.1297 / % possible all: 85.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.51 Å27.28 Å
Translation2.51 Å27.28 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OQT

2oqt


Resolution: 2.4→27.28 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.265 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.114 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 835 14 %RANDOM
Rwork0.154 ---
all0.191 6170 --
obs0.166 5982 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.719 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.48 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: LAST / Resolution: 2.4→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 0 45 1248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221228
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9851670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.46225.10647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38515214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.65154
X-RAY DIFFRACTIONr_chiral_restr0.1330.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02902
X-RAY DIFFRACTIONr_nbd_refined0.220.2503
X-RAY DIFFRACTIONr_nbtor_refined0.310.2849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.25
X-RAY DIFFRACTIONr_mcbond_it1.1351.5798
X-RAY DIFFRACTIONr_mcangle_it1.77321270
X-RAY DIFFRACTIONr_scbond_it3.083478
X-RAY DIFFRACTIONr_scangle_it5.3134.5400
LS refinement shellResolution: 2.397→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 44 -
Rwork0.157 272 -
all-316 -
obs-316 75.06 %

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