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- PDB-4xz6: TmoX in complex with TMAO -

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Basic information

Entry
Database: PDB / ID: 4xz6
TitleTmoX in complex with TMAO
ComponentsGlycine betaine/proline ABC transporter, periplasmic substrate-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / substrate binding protein / complex
Function / homologyABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / metal ion binding / trimethylamine oxide / Glycine betaine/proline ABC transporter, periplasmic substrate-binding protein
Function and homology information
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, Y.Z. / Li, C.Y.
CitationJournal: J.Bacteriol. / Year: 2015
Title: Mechanistic Insight into Trimethylamine N-Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3
Authors: Li, C.Y. / Chen, X.L. / Shao, X. / Wei, T.D. / Wang, P. / Xie, B.B. / Qin, Q.L. / Zhang, X.Y. / Su, H.N. / Song, X.Y. / Shi, M. / Zhou, B.C. / Zhang, Y.Z.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine betaine/proline ABC transporter, periplasmic substrate-binding protein
B: Glycine betaine/proline ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2069
Polymers74,6692
Non-polymers5377
Water2,954164
1
A: Glycine betaine/proline ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6345
Polymers37,3351
Non-polymers2994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area12050 Å2
MethodPISA
2
B: Glycine betaine/proline ABC transporter, periplasmic substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5724
Polymers37,3351
Non-polymers2373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.624, 134.979, 58.366
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycine betaine/proline ABC transporter, periplasmic substrate-binding protein


Mass: 37334.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (bacteria)
Strain: ATCC 700808 / DSM 15171 / DSS-3 / Gene: SPO1548 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LT66

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.56 Å3/Da / Density % sol: 21.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris (pH 5.5) and 25% (wt/vol) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23366 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.11
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.751 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
HKL-2000data processing
HKL-2000data scaling
SHELXDEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→44.15 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 0 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 1140 5.15 %
Rwork0.174 --
obs0.177 22143 94.5 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.91 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.9784 Å20 Å2-7.1832 Å2
2--0.7478 Å20 Å2
3----12.7262 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 32 164 4718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074709
X-RAY DIFFRACTIONf_angle_d1.0536444
X-RAY DIFFRACTIONf_dihedral_angle_d15.1981636
X-RAY DIFFRACTIONf_chiral_restr0.071670
X-RAY DIFFRACTIONf_plane_restr0.005847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1943-2.29420.31131140.21322458X-RAY DIFFRACTION88
2.2942-2.41510.31351350.20442480X-RAY DIFFRACTION90
2.4151-2.56640.28911290.19722555X-RAY DIFFRACTION93
2.5664-2.76450.25571360.2072626X-RAY DIFFRACTION94
2.7645-3.04270.28591640.19562625X-RAY DIFFRACTION96
3.0427-3.48280.21431630.17182716X-RAY DIFFRACTION98
3.4828-4.38730.20321400.13482758X-RAY DIFFRACTION98
4.3873-44.15580.2141590.16412785X-RAY DIFFRACTION100

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