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- PDB-3ttl: Crystal structure of apo-SpuE -

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Basic information

Entry
Database: PDB / ID: 3ttl
TitleCrystal structure of apo-SpuE
ComponentsPolyamine transport protein
KeywordsTRANSPORT PROTEIN / polyamine binding / 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-binding periplasmic protein SpuE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWu, D.H. / Lim, S.C. / 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 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)75,0072
Polymers75,0072
Non-polymers00
Water3,693205
1
A: Polyamine transport protein


Theoretical massNumber of molelcules
Total (without water)37,5031
Polymers37,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyamine transport protein


Theoretical massNumber of molelcules
Total (without water)37,5031
Polymers37,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.323, 48.841, 114.334
Angle α, β, γ (deg.)90.00, 103.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyamine transport protein


Mass: 37503.406 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 0.2M MgCl2, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 18, 2009
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→38.51 Å / Num. all: 30162 / Num. obs: 30162 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.42 Å / % possible all: 79.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
REFMAC5.4.0077refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TTN

3ttn


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.449 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26997 1508 5 %RANDOM
Rwork0.21807 ---
all0.2207 28592 --
obs0.2207 28592 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.787 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å2-0.32 Å2
2--0.17 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5236 0 0 205 5441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225368
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9677306
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00625.339236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60515878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1291514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214104
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_it0.6891.53344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33625384
X-RAY DIFFRACTIONr_scbond_it1.93632024
X-RAY DIFFRACTIONr_scangle_it3.1684.51922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 82 -
Rwork0.29 1587 -
obs--74.48 %

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