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- PDB-3rot: Crystal structure of ABC sugar transporter (periplasmic sugar bin... -

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Basic information

Entry
Database: PDB / ID: 3rot
TitleCrystal structure of ABC sugar transporter (periplasmic sugar binding protein) from Legionella pneumophila
ComponentsABC sugar transporter, periplasmic sugar binding protein
KeywordsTRANSPORT PROTEIN / NYSGRC / PSI-BIOLOGY / Structural Genomics / New York Structural Genomics Research Consortium / carbohydrate transport
Function / homology
Function and homology information


cell envelope / transmembrane transport / carbohydrate binding
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC sugar transporter, periplasmic sugar binding protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsEswaramoorthy, S. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of ABC sugar transporter (periplasmic sugar binding protein) from Legionella pneumophila
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC sugar transporter, periplasmic sugar binding protein
B: ABC sugar transporter, periplasmic sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2384
Polymers68,0542
Non-polymers1842
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ABC sugar transporter, periplasmic sugar binding protein
hetero molecules

B: ABC sugar transporter, periplasmic sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2384
Polymers68,0542
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area2320 Å2
ΔGint-13 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.693, 117.860, 54.607
Angle α, β, γ (deg.)90.00, 107.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ABC sugar transporter, periplasmic sugar binding protein


Mass: 34026.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0184 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5ZZ27
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 6000, 5% MPD, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 44651 / Num. obs: 44651 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.1
Reflection shellResolution: 1.91→1.97 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.667 / Num. unique all: 3410 / % possible all: 90.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→43.23 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 127422.05 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED, BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1716 4.1 %RANDOM
Rwork0.22 ---
all0.239 42026 --
obs0.22 42026 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.7848 Å2 / ksol: 0.340373 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.76 Å20 Å212.95 Å2
2---13.07 Å20 Å2
3---6.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 1.91→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4308 0 12 91 4411
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.83
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 216 4.1 %
Rwork0.344 5020 -
obs-5236 68.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4GOL5-coot-par.txtGOL5-coot-top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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