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- PDB-2hzk: Crystal structures of a sodium-alpha-keto acid binding subunit fr... -

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Basic information

Entry
Database: PDB / ID: 2hzk
TitleCrystal structures of a sodium-alpha-keto acid binding subunit from a TRAP transporter in its open form
ComponentsTRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
KeywordsLIGAND BINDING / TRANSPORT PROTEIN / TRAP Transporter / periplasmic subunit
Function / homology
Function and homology information


organic acid transport / tripartite ATP-independent periplasmic transporter complex / : / organic acid binding / transmembrane transport / periplasmic space / protein homodimerization activity / metal ion binding
Similarity search - Function
Alpha-keto acid binding periplasmic protein / Solute binding protein, TakP-like / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Alpha-keto acid binding periplasmic protein / Solute binding protein, TakP-like / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-keto acid-binding periplasmic protein TakP
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsGonin, S. / Arnoux, P. / Pierru, B. / Alonso, B. / Sabaty, M. / Pignol, D.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding.
Authors: Gonin, S. / Arnoux, P. / Pierru, B. / Lavergne, J. / Alonso, B. / Sabaty, M. / Pignol, D.
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 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: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
B: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
C: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
D: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,3218
Polymers161,9524
Non-polymers3684
Water13,169731
1
A: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
B: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1604
Polymers80,9762
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-55 kcal/mol
Surface area22890 Å2
MethodPISA
2
C: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
D: TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1604
Polymers80,9762
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-55 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.505, 63.826, 127.897
Angle α, β, γ (deg.)90.00, 106.58, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer

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Components

#1: Protein
TRAP-T family sorbitol/mannitol transporter, periplasmic binding protein, SmoM


Mass: 40488.070 Da / Num. of mol.: 4 / Fragment: SkaP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Species: Rhodobacter sphaeroides / Strain: ATCC 17023 / Plasmid: pET101 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3J1R2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 100 mM sodium citrate 1.5M ammonium sulfate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97940,0.97960,0.97565
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2006
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
30.975651
ReflectionResolution: 1.7→60 Å / Num. all: 177747 / Num. obs: 175128 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7→1.71 Å / % possible all: 95.5

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97947.32-8.57
13 wavelength20.97963.38-10.38
13 wavelength30.97574.2-4.85
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se14.6250.7380.50.090.724
2Se15.990.6120.3930.3261.048
3Se12.740.3620.890.2470.901
4Se14.0730.7970.5530.2020.874
5Se16.0050.6920.6370.330.812
6Se14.2280.2930.8130.3970.723
7Se14.3170.8520.3820.2140.969
8Se18.2470.0510.8850.1580.73
9Se19.8610.7290.5440.390.951
10Se18.930.610.5820.2750.866
11Se23.1980.0820.8910.0950.583
12Se25.0530.8260.3880.4770.758
13Se13.4490.7360.7450.2560.856
14Se15.420.2790.9820.1770.998
15Se23.9290.0880.9890.2820.839
16Se24.2960.1310.1230.0330.671
17Se21.070.6840.8520.1660.848
18Se21.3680.0630.7530.2440.923
19Se26.2330.6390.4380.4620.964
20Se12.9910.7310.2790.2920.62
21Se21.1860.3170.8560.0980.9
22Se21.4340.0740.0150.2070.837
23Se21.0390.140.1090.140.987
24Se18.0340.7910.2550.2230.767
25Se21.5150.330.7380.2690.856
26Se15.7390.2240.7360.290.785
27Se31.3170.040.8150.3460.916
28Se32.4190.6490.8260.1570.89
29Se20.920.8530.2220.3740.621
30Se34.060.6070.8760.1710.807
31Se30.4780.0370.7560.3390.802
32Se27.1570.9860.8620.3330.692
33Se30.590.60.630.2030.758
34Se28.8590.6680.3670.4420.748
35Se41.7970.8360.3260.0161.005
36Se22.8790.5890.6410.0730.497
37Se24.990.6420.3230.4270.564
38Se36.4760.0520.0860.0070.694
39Se37.5670.1090.0680.0230.693
Phasing dmFOM centric: 0.69 / Reflection centric: 4984
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-19.9680.950.950.8947884218570
3.6-5.70.950.950.881471213753959
2.9-3.60.880.890.771843017540890
2.5-2.90.80.810.651851517762753
2.1-2.50.690.690.5632885317181167
2-2.10.510.520.42040019755645

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Processing

Software
NameVersionClassificationNB
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→60 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.725 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 8721 5 %RANDOM
Rwork0.179 ---
all0.18 177747 --
obs0.18 175128 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.167 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.3 Å2
2--0.33 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10511 0 24 731 11266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210886
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9314809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57551349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01324.308506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.182151635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.531536
X-RAY DIFFRACTIONr_chiral_restr0.1080.21526
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028536
X-RAY DIFFRACTIONr_nbd_refined0.2060.25484
X-RAY DIFFRACTIONr_nbtor_refined0.3090.27485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2676
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.225
X-RAY DIFFRACTIONr_mcbond_it1.0581.56860
X-RAY DIFFRACTIONr_mcangle_it1.261210654
X-RAY DIFFRACTIONr_scbond_it2.39334815
X-RAY DIFFRACTIONr_scangle_it3.2964.54153
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 623 -
Rwork0.257 11753 -
obs-12376 94.94 %

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