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- PDB-3ttn: Crystal structures of polyamine receptors SpuD and SpuE from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3ttn
TitleCrystal structures of polyamine receptors SpuD and SpuE from Pseudomonas aeruginosa
ComponentsPolyamine transport protein
KeywordsTRANSPORT PROTEIN / polyamine binding protein / spermidine
Function / homology
Function and homology information


polyamine transport / spermidine binding / periplasmic space / extracellular space
Similarity search - Function
Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SPERMIDINE / Spermidine-binding periplasmic protein SpuE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLim, S.C. / Wu, D.H. / Song, H.W.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural Basis of Substrate Binding Specificity Revealed by the Crystal Structures of Polyamine Receptors SpuD and SpuE from Pseudomonas aeruginosa
Authors: Wu, D.H. / Lim, S.C. / Dong, Y.H. / Wu, J.E. / Tao, F. / Zhou, L. / Zhang, L.H. / Song, H.W.
History
DepositionSep 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyamine transport protein
B: Polyamine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7664
Polymers75,4762
Non-polymers2902
Water3,549197
1
A: Polyamine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8832
Polymers37,7381
Non-polymers1451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyamine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8832
Polymers37,7381
Non-polymers1451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.329, 44.367, 81.553
Angle α, β, γ (deg.)91.50, 95.24, 95.23
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B35 - 355
2114A35 - 355

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Components

#1: Protein Polyamine transport protein


Mass: 37737.875 Da / Num. of mol.: 2 / Fragment: UNP residues 28-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: spuE / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6J0
#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 2.6
Details: 0.1M citric acid, 28% PEG 6000, 4% Jeffamine M-600, pH 2.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.97988 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97988 Å / Relative weight: 1
ReflectionResolution: 2→24.07 Å / Num. all: 40146 / Num. obs: 40146 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.11 Å / % possible all: 87.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SHELXSphasing
REFMAC5.4.0077refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→23.07 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.897 / SU B: 4.527 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24369 2034 5.1 %RANDOM
Rwork0.2116 ---
obs0.21328 38108 96.59 %-
all-38108 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.838 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.08 Å2-0.01 Å2
2---0 Å2-0.02 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2→23.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5201 0 20 197 5418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225349
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.977272
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1045662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50625.362235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79615871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9361514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214074
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5591.53319
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0425344
X-RAY DIFFRACTIONr_scbond_it1.75532030
X-RAY DIFFRACTIONr_scangle_it2.8424.51928
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 2 / Auth asym-ID: A / Ens-ID: 1 / Number: 2465 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.30.5
medium thermal0.392
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 120 -
Rwork0.217 2274 -
obs--78.26 %

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