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- PDB-3bed: Mannose/sorbose specific IIA subunit of phosphotransferase system... -

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Basic information

Entry
Database: PDB / ID: 3bed
TitleMannose/sorbose specific IIA subunit of phosphotransferase system from Enterococcus faecalis
ComponentsPTS system, IIA component
KeywordsTRANSFERASE / MANNOSE/SORBOSE / PHOSPHOTRANSFERASE SYSTEM / STRUCTURAL GENOMICS / APC28805 / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / transferase activity / membrane
Similarity search - Function
: / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system, IIA component
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsOsipiuk, J. / Wu, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-Ray Crystal Structure of Mannose/sorbose specific IIa subunit of phosphotransferase system from Enterococcus faecalis.
Authors: Osipiuk, J. / Wu, R. / Moy, S. / Joachimiak, A.
History
DepositionNov 16, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionNov 27, 2007ID: 2IAC
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 999 SEQUENCE LYSINE RESIDUES OF THE PROTEIN WERE CHEMICALLY DIMETHYLATED AFTER PROTEIN PURIFICATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTS system, IIA component
B: PTS system, IIA component


Theoretical massNumber of molelcules
Total (without water)30,6082
Polymers30,6082
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
MethodPISA
2
A: PTS system, IIA component
B: PTS system, IIA component

A: PTS system, IIA component
B: PTS system, IIA component


Theoretical massNumber of molelcules
Total (without water)61,2174
Polymers61,2174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.059, 37.503, 76.993
Angle α, β, γ (deg.)90.00, 121.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-148-

HOH

21A-188-

HOH

31A-207-

HOH

DetailsAuthors state that the biological unit of this protein is unknown.

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Components

#1: Protein PTS system, IIA component


Mass: 15304.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_0461 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q838I6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M CALCIUM CHLORIDE, 0.1 M HEPES BUFFER, 30% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2006
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→37.5 Å / Num. all: 36836 / Num. obs: 36836 / % possible obs: 79.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 35.3
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.18 / Num. unique all: 973 / % possible all: 31.8

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Processing

Software
NameVersionClassification
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→37.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.626 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.104 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 1872 5.1 %RANDOM
Rwork0.1573 ---
all0.1593 34957 --
obs0.1593 34957 79.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.158 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å2-1.24 Å2
2--3.39 Å20 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 1.45→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 0 330 2206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222068
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8052.022852
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.37427.57666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.128155
X-RAY DIFFRACTIONr_chiral_restr0.3320.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021493
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.21196
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21485
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6971.51433
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13622258
X-RAY DIFFRACTIONr_scbond_it4.7323699
X-RAY DIFFRACTIONr_scangle_it5.4184.5569
X-RAY DIFFRACTIONr_rigid_bond_restr4.06532132
X-RAY DIFFRACTIONr_sphericity_free6.6483330
X-RAY DIFFRACTIONr_sphericity_bonded4.2832025
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 53 -
Rwork0.187 1029 -
obs-1082 32.01 %

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