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- PDB-3ttk: Crystal structure of apo-SpuD -

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Basic information

Entry
Database: PDB / ID: 3ttk
TitleCrystal structure of apo-SpuD
ComponentsPolyamine transport protein
KeywordsTRANSPORT PROTEIN / polyamine receptor / polyamine binding
Function / homology
Function and homology information


polyamine transport / putrescine binding / periplasmic 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
Putrescine-binding periplasmic protein SpuD
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.97 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Polyamine transport protein


Theoretical massNumber of molelcules
Total (without water)115,1423
Polymers115,1423
Non-polymers00
Water2,378132
1
A: Polyamine transport protein


Theoretical massNumber of molelcules
Total (without water)38,3811
Polymers38,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyamine transport protein


Theoretical massNumber of molelcules
Total (without water)38,3811
Polymers38,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Polyamine transport protein


Theoretical massNumber of molelcules
Total (without water)38,3811
Polymers38,3811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.769, 108.983, 228.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polyamine transport protein / polyamine binding protein


Mass: 38380.617 Da / Num. of mol.: 3 / Fragment: UNP residues 26-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: spuD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6J1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.1M Mes, pH 6.5, 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 15, 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: 2.9→20 Å / Num. all: 23272 / Num. obs: 23272 / % possible obs: 84.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→3.06 Å / % possible all: 80.9

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Processing

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

3ttm


Resolution: 2.97→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.853 / SU B: 20.282 / SU ML: 0.379 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.577 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28794 1086 5 %RANDOM
Rwork0.21517 ---
all0.21876 20613 --
obs0.21876 20613 85.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.859 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å2-0 Å2-0 Å2
2---1.52 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8025 0 0 132 8157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228229
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.96811178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31451017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91125.678354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0611515
X-RAY DIFFRACTIONr_chiral_restr0.0710.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216216
X-RAY DIFFRACTIONr_mcbond_it0.351.55103
X-RAY DIFFRACTIONr_mcangle_it0.6528268
X-RAY DIFFRACTIONr_scbond_it0.59233126
X-RAY DIFFRACTIONr_scangle_it1.0554.52910
LS refinement shellResolution: 2.97→3.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 65 -
Rwork0.331 1364 -
obs--79.61 %

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