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- PDB-2r48: Crystal structure of the fructose specific IIB subunit of PTS sys... -

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Basic information

Entry
Database: PDB / ID: 2r48
TitleCrystal structure of the fructose specific IIB subunit of PTS system from Bacillus subtilis subsp. subtilis str. 168
ComponentsPhosphotransferase system (PTS) mannose-specific enzyme IIBCA componentPEP group translocation
KeywordsTRANSFERASE / TRANSPORT PROTEIN / PTS system / phosphotransferase system / fructose specific IIB subunit / pfam02379 / PSI-2 / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / Membrane / Sugar transport / Transmembrane / Transport
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-mannose phosphotransferase / protein-phosphocysteine-sugar phosphotransferase activity / carbohydrate:proton symporter activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Phosphotransferase system, IIA component fructose subfamily / Phosphotransferase system, fructose IIC component / Phosphotransferase system, fructose-specific IIB subunit / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphotransferase system, EIIC ...Phosphotransferase system, IIA component fructose subfamily / Phosphotransferase system, fructose IIC component / Phosphotransferase system, fructose-specific IIB subunit / Phosphotransferase system, EIIC component, type 2 / PTS_EIIC type-2 domain profile. / PTS EIIA domains phosphorylation site signature 2. / Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / PTS EIIA type-2 domain / Phosphotransferase system, EIIC / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / Phosphotransferase system, EIIC / PTS_EIIA type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Phosphotransferase/anion transporter / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system mannose-specific EIIBCA component
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsNocek, B. / Cuff, M. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the fructose specific IIB subunit of PTS system from Bacillus subtilis subsp. subtilis str. 168.
Authors: Nocek, B. / Cuff, M. / Sather, A. / Clancy, S. / Joachimiak, A.
History
DepositionAug 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphotransferase system (PTS) mannose-specific enzyme IIBCA component


Theoretical massNumber of molelcules
Total (without water)11,4771
Polymers11,4771
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.931, 48.931, 68.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-126-

HOH

DetailsAccording to authors, the crystal packing indicates that dimer could be the biologically relevant oligomerization state.

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Components

#1: Protein Phosphotransferase system (PTS) mannose-specific enzyme IIBCA component / PEP group translocation


Mass: 11476.965 Da / Num. of mol.: 1 / Fragment: Residues 2-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Species: Bacillus subtilis / Strain: 168 / Gene: manP, BSU12010 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O31645
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.78 Å3/Da / Density % sol: 30.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97950, 0.97960
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2007 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
ReflectionResolution: 1.8→40 Å / Num. all: 7790 / Num. obs: 7790 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.7
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.3 / % possible all: 61.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.8→39.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.62 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23743 361 4.7 %RANDOM
Rwork0.18328 ---
all0.1871 7785 --
obs0.18601 7402 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.628 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2--1.57 Å20 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms795 0 0 57 852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022805
X-RAY DIFFRACTIONr_bond_other_d0.0110.02550
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9891086
X-RAY DIFFRACTIONr_angle_other_deg1.03331360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29225.88234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80515155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.832155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02137
X-RAY DIFFRACTIONr_nbd_refined0.2030.2159
X-RAY DIFFRACTIONr_nbd_other0.2070.2556
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2392
X-RAY DIFFRACTIONr_nbtor_other0.0890.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1711.5629
X-RAY DIFFRACTIONr_mcbond_other0.2671.5216
X-RAY DIFFRACTIONr_mcangle_it1.4172838
X-RAY DIFFRACTIONr_scbond_it2.4533300
X-RAY DIFFRACTIONr_scangle_it3.5194.5247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 13 -
Rwork0.256 359 -
obs--65.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6179-3.46154.6227.9656-7.76116.4570.094-0.1794-0.22120.2578-0.1483-0.48070.03450.48650.05430.1251-0.0642-0.05250.14260.00650.144113.93217.127720.1301
25.0906-0.816-9.54120.53352.514220.29130.48760.4491-0.1222-0.6574-0.20860.2103-1.4826-0.7701-0.2790.2730.0634-0.04130.19790.07330.09715.173116.46063.1306
33.6193-2.3206-1.361.64980.04234.7648-0.0280.2722-0.13860.06580.0530.0328-0.22520.3266-0.0250.1309-0.04950.00270.2012-0.02440.064512.466311.51285.0293
44.3642-2.6329-0.691310.7034-6.56579.73030.11890.47240.1149-0.5788-0.2735-0.16480.9969-0.18770.15460.1145-0.0289-0.02680.1989-0.03950.074919.2296.813212.0649
520.1694-0.60311.41491.5174-1.95112.52940.28660.2759-0.4066-0.0574-0.1032-0.03150.05790.2533-0.18340.1191-0.0044-0.02990.1296-0.08220.105816.51475.914916.1082
612.9077-2.12698.568116.8084-5.5926.7492-0.00590.86550.1718-0.89420.33880.53870.33770.5316-0.33290.1227-0.0466-0.03190.20060.06220.0950.964510.24657.3578
71.2511-2.28223.16366.0429-2.645934.3763-0.00660.1042-0.2526-0.37270.3250.20750.0422-0.8866-0.31840.0541-0.0497-0.02680.11360.01510.14193.28674.306514.326
815.32472.343214.345615.45450.778813.56160.188-0.9389-0.47090.6321-0.19150.54380.0261-0.5540.00350.1083-0.03840.04040.11070.0670.13153.97833.105325.1406
91.26910.98280.46552.8351-4.05679.5780.0046-0.09340.12340.03170.11240.0117-0.1417-0.0593-0.11710.1551-0.0241-0.00370.0958-0.00330.07988.454314.103817.9965
105.61480.67922.43333.3661-6.48417.7920.0157-0.15940.04560.44540.33230.4401-0.9211-0.0938-0.34790.13530.02870.05420.11110.00710.09531.316214.467722.1823
111.6040.6606-0.85642.7049-3.00238.42460.1168-0.06430.1380.15040.16020.0498-0.20980.0277-0.2770.1457-0.0389-0.0070.123-0.03130.081810.671717.385520.115
1213.09020.92074.12235.59262.17819.15830.20520.07920.2494-0.70860.1443-0.0892-1.02640.9109-0.34950.1713-0.10090.08220.2219-0.01130.070616.964119.1977.7891
134.7936-1.33294.51683.4697-2.498133.147-0.16190.2423-0.14520.23470.0903-0.5422-0.74770.73970.07160.0232-0.0792-0.02160.1651-0.03940.11120.609615.525317.9873
1441.6031-2.71723.86887.1482-3.62017.4387-0.6178-1.03721.53520.29310.1069-0.876-0.0898-0.33320.5110.07480.073-0.01860.067-0.1130.140912.57918.617527.5104
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 72 - 9
2X-RAY DIFFRACTION2AA8 - 1410 - 16
3X-RAY DIFFRACTION3AA15 - 2217 - 24
4X-RAY DIFFRACTION4AA23 - 2825 - 30
5X-RAY DIFFRACTION5AA29 - 3731 - 39
6X-RAY DIFFRACTION6AA38 - 4440 - 46
7X-RAY DIFFRACTION7AA45 - 4947 - 51
8X-RAY DIFFRACTION8AA50 - 5452 - 56
9X-RAY DIFFRACTION9AA55 - 6657 - 68
10X-RAY DIFFRACTION10AA67 - 7469 - 76
11X-RAY DIFFRACTION11AA75 - 8277 - 84
12X-RAY DIFFRACTION12AA83 - 8785 - 89
13X-RAY DIFFRACTION13AA88 - 9790 - 99
14X-RAY DIFFRACTION14AA98 - 104100 - 106

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