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- PDB-2r4q: The structure of a domain of fruA from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2r4q
TitleThe structure of a domain of fruA from Bacillus subtilis
ComponentsPhosphotransferase system (PTS) fructose-specific enzyme IIABC componentPEP group translocation
KeywordsTRANSFERASE / TRANSPORT PROTEIN / Phosphotransferase system / Fructose specific IIB subunit / pfam02379 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Membrane / Sugar transport / Transmembrane / Transport
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-fructose phosphotransferase / protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity / protein-phosphocysteine-sugar phosphotransferase activity / carbohydrate:proton symporter activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / 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 / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 ...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 / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / 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 fructose-specific EIIABC component
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsCuff, M.E. / Sather, A. / Nocek, B. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a domain of fruA from Bacillus subtilis.
Authors: Cuff, M.E. / Sather, A. / Nocek, B. / Clancy, S. / Joachimiak, A.
History
DepositionAug 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotransferase system (PTS) fructose-specific enzyme IIABC component


Theoretical massNumber of molelcules
Total (without water)11,6101
Polymers11,6101
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.661, 43.661, 110.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-289-

HOH

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

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Components

#1: Protein Phosphotransferase system (PTS) fructose-specific enzyme IIABC component / PEP group translocation / Fructose PTS IIABC


Mass: 11609.996 Da / Num. of mol.: 1 / Fragment: Targeted domain: Residues 171-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Species: Bacillus subtilis / Strain: 168 / Gene: fruA, BSU14400 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P71012
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921, 0.97940
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 5, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.97941
ReflectionRedundancy: 11.4 % / Av σ(I) over netI: 12.3 / Number: 167802 / Rmerge(I) obs: 0.063 / Χ2: 1.97 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 14676 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.955090.810.0576.2610.9
3.133.9597.510.0493.55512.1
2.743.1398.510.0593.08912.7
2.492.7498.810.0652.43513.1
2.312.4999.510.0671.97813.1
2.172.3199.610.0691.64713.2
2.062.1799.810.081.50713.3
1.972.0699.710.0911.28813.3
1.91.9799.910.1081.18513.4
1.831.910010.1391.0113.5
1.771.8310010.1880.90912.5
1.721.7710010.2290.8529.4
1.681.7299.810.2850.7297.9
1.641.6897.710.330.7076.7
1.61.6490.810.4040.6945.6
ReflectionResolution: 1.6→50 Å / Num. all: 14676 / Num. obs: 14676 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.974 / Net I/σ(I): 12.3
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.3 / Num. unique all: 876 / Χ2: 0.694 / % possible all: 90.8

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.6 Å / D res low: 40.62 Å / FOM : 0.401 / FOM acentric: 0.445 / FOM centric: 0.198 / Reflection: 14650 / Reflection acentric: 12051 / Reflection centric: 2599
Phasing MAD set

Highest resolution: 1.6 Å / Lowest resolution: 40.62 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.8510.10.100120512599
20.940.882.33.30.50.44119762551
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
110.03-40.621.410.40.2001944
15.72-10.031.6910.40.200167121
14-5.721.3710.30.200457183
13.08-41.1910.20.200883283
12.5-3.081.7410.10.1001446370
12.11-2.51.910.10002164462
11.82-2.113.09100002990539
11.6-1.8218.68100003925597
210.03-40.620.790.585.63.61.041.631944
25.72-10.030.690.623.34.11.581.16166120
24-5.720.750.683.33.91.170.99457178
23.08-40.840.852.53.51.10.68883282
22.5-3.080.880.871.92.90.910.541446370
22.11-2.50.960.961.930.580.362164445
21.82-2.110.990.981.930.350.22989536
21.6-1.82112.73.70.150.093852576
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se25.434150.4730.9330.1110
2Se33.397660.2361.2680.0280
3Se24.249190.3061.280.1890
4Se55.811960.2671.2510.1970
5Se22.907970.4720.9330.111-0.046
6Se33.008280.2361.2680.028-0.055
7Se23.797840.3061.280.189-0.015
8Se56.886120.2671.250.197-0.036
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10.03-40.620.4890.650.419631944
5.72-10.030.6990.8170.536288167121
4-5.720.6620.7430.459640457183
3.08-40.6260.7180.3391166883283
2.5-3.080.5990.6810.27618161446370
2.11-2.50.5030.5750.16526262164462
1.82-2.110.3890.4420.09735292990539
1.6-1.820.1550.1740.03245223925597
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 14650
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.08-10042.40.841502
3.99-5.0845.10.895502
3.47-3.9949.60.883512
3.14-3.4749.40.873507
2.91-3.1448.70.857503
2.74-2.91440.908509
2.6-2.74490.879519
2.48-2.648.70.876511
2.38-2.4850.20.893506
2.3-2.3851.30.879516
2.22-2.354.40.884540
2.15-2.2251.80.88560
2.09-2.1552.90.892551
2.03-2.0955.70.899605
1.98-2.03550.875590
1.93-1.9856.90.856605
1.88-1.9358.80.845629
1.84-1.8863.70.85639
1.8-1.8466.30.815660
1.76-1.868.30.821667
1.73-1.7674.10.811673
1.69-1.7374.30.828700
1.66-1.6976.40.825696
1.63-1.6677.40.787689
1.6-1.6381.70.791759

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.6→23.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.557 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 740 5.1 %RANDOM
Rwork0.198 ---
all0.2 14648 --
obs0.2 14648 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 0 209 984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022858
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9891165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4075118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12225.93832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17115173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.765154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02630
X-RAY DIFFRACTIONr_nbd_refined0.210.2430
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.236
X-RAY DIFFRACTIONr_mcbond_it0.8451.5573
X-RAY DIFFRACTIONr_mcangle_it1.2732907
X-RAY DIFFRACTIONr_scbond_it2.663310
X-RAY DIFFRACTIONr_scangle_it4.3424.5255
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 61 -
Rwork0.295 909 -
all-970 -
obs--91.51 %
Refinement TLS params.Method: refined / Origin x: 3.3997 Å / Origin y: 23.6758 Å / Origin z: -5.7741 Å
111213212223313233
T-0.0884 Å2-0.017 Å20.0145 Å2--0.1487 Å20.0045 Å2---0.13 Å2
L2.1998 °2-0.0902 °20.0982 °2-2.2209 °2-0.227 °2--3.3047 °2
S0.0888 Å °-0.0527 Å °-0.0795 Å °-0.2556 Å °-0.1132 Å °0.0126 Å °0.0586 Å °0.0772 Å °0.0244 Å °

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