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- PDB-6ikm: Crystal structure of SpuE-Spermidine in complex with ScFv5 -

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Basic information

Entry
Database: PDB / ID: 6ikm
TitleCrystal structure of SpuE-Spermidine in complex with ScFv5
Components
  • Polyamine transport protein
  • ScFv5
KeywordsANTIMICROBIAL PROTEIN / Type three secretion system / antibody / SpuE / ATP binding cassette
Function / homology
Function and homology information


polyamine binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
SPERMIDINE / Extracellular solute-binding protein / Spermidine-binding periplasmic protein SpuE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.398 Å
AuthorsWu, D. / Sun, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31771006 China
CitationJournal: J.Mol.Biol. / Year: 2019
Title: A Potent Anti-SpuE Antibody Allosterically Inhibits Type III Secretion System and Attenuates Virulence of Pseudomonas Aeruginosa.
Authors: Zhang, Y. / Sun, X. / Qian, Y. / Yi, H. / Song, K. / Zhu, H. / Zonta, F. / Chen, W. / Ji, Q. / Miersch, S. / Sidhu, S.S. / Wu, D.
History
DepositionOct 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Nov 13, 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
a: ScFv5
B: Polyamine transport protein
b: ScFv5
C: Polyamine transport protein
c: ScFv5
D: Polyamine transport protein
d: ScFv5
E: Polyamine transport protein
e: ScFv5
F: Polyamine transport protein
f: ScFv5
G: Polyamine transport protein
g: ScFv5
H: Polyamine transport protein
h: ScFv5
I: Polyamine transport protein
i: ScFv5
J: Polyamine transport protein
j: ScFv5
K: Polyamine transport protein
k: ScFv5
L: Polyamine transport protein
l: ScFv5
M: Polyamine transport protein
m: ScFv5
N: Polyamine transport protein
n: ScFv5
O: Polyamine transport protein
o: ScFv5
P: Polyamine transport protein
p: ScFv5
Q: Polyamine transport protein
q: ScFv5
R: Polyamine transport protein
r: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,169,817108
Polymers1,162,01536
Non-polymers7,80272
Water00
1
A: Polyamine transport protein
a: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyamine transport protein
b: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0867
Polymers64,5562
Non-polymers5295
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyamine transport protein
c: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polyamine transport protein
d: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Polyamine transport protein
e: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0867
Polymers64,5562
Non-polymers5295
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Polyamine transport protein
f: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Polyamine transport protein
g: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8945
Polymers64,5562
Non-polymers3373
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Polyamine transport protein
h: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8945
Polymers64,5562
Non-polymers3373
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Polyamine transport protein
i: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Polyamine transport protein
j: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Polyamine transport protein
k: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Polyamine transport protein
l: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Polyamine transport protein
m: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Polyamine transport protein
n: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2789
Polymers64,5562
Non-polymers7227
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Polyamine transport protein
o: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2789
Polymers64,5562
Non-polymers7227
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Polyamine transport protein
p: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7023
Polymers64,5562
Non-polymers1451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
Q: Polyamine transport protein
q: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7023
Polymers64,5562
Non-polymers1451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
R: Polyamine transport protein
r: ScFv5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9906
Polymers64,5562
Non-polymers4334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.235, 481.804, 146.134
Angle α, β, γ (deg.)90.000, 120.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Polyamine transport protein / Spermidine-binding periplasmic protein SpuE


Mass: 37503.406 Da / Num. of mol.: 18 / Fragment: UNP residues 28-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: A0A069QID4, UniProt: Q9I6J0*PLUS
#2: Antibody
ScFv5


Mass: 27053.006 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Spermidine-binding periplasmic protein SpuE


Mass: 96.063 Da / Num. of mol.: 54 / Fragment: UNP residues 28-362
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C7H19N3
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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris, pH 5.5, 0.2M Li2SO4, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 235574 / % possible obs: 98.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 63.43 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.069 / Rrim(I) all: 0.152 / Χ2: 0.945 / Net I/σ(I): 5.1 / Num. measured all: 1084709
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.523.40.569208360.7940.3270.6610.99787.6
3.52-3.664.20.491236870.9020.2620.5590.99399
3.66-3.834.60.396237810.9380.2010.4460.999100
3.83-4.034.50.27238750.9550.1380.3051.02399.9
4.03-4.284.90.192238270.9820.0950.2151.00499.9
4.28-4.6150.154238680.9840.0760.1720.98699.9
4.61-5.084.80.124238630.9860.0620.1390.955100
5.08-5.814.80.111239040.9870.0560.1250.903100
5.81-7.324.90.091239510.990.0450.1020.837100
7.32-504.70.06239820.9930.0310.0670.78699.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TTN, 4BUH

3ttn

4buh


Resolution: 3.398→46.473 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 10741 5.03 %
Rwork0.2281 202966 -
obs0.2301 213707 89.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.43 Å2 / Biso mean: 57.0952 Å2 / Biso min: 32.55 Å2
Refinement stepCycle: final / Resolution: 3.398→46.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77706 0 450 0 78156
Biso mean--60.5 --
Num. residues----10080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00979992
X-RAY DIFFRACTIONf_angle_d1.155108740
X-RAY DIFFRACTIONf_chiral_restr0.08711880
X-RAY DIFFRACTIONf_plane_restr0.00613914
X-RAY DIFFRACTIONf_dihedral_angle_d15.62129019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3982-3.43680.38191290.34372552268135
3.4368-3.47720.35451540.32332962311638
3.4772-3.51960.3371840.3233448363246
3.5196-3.56410.33932270.30653837406451
3.5641-3.6110.32652640.30484668493263
3.611-3.66040.3352920.29715721601375
3.6604-3.71270.34623550.30046680703590
3.7127-3.76810.3373810.30027374775597
3.7681-3.8270.3313820.29067530791299
3.827-3.88970.31263880.27737428781699
3.8897-3.95670.34173810.26476408021100
3.9567-4.02860.29593730.258875157888100
4.0286-4.10610.27333850.237974787863100
4.1061-4.18980.28434100.234676128022100
4.1898-4.28090.27664070.22275267933100
4.2809-4.38040.25123920.223275457937100
4.3804-4.48980.26293730.220175617934100
4.4898-4.61110.2664100.221475777987100
4.6111-4.74670.25494340.208675027936100
4.7467-4.89970.24714030.21176108013100
4.8997-5.07460.26114360.217674747910100
5.0746-5.27750.25943670.215475757942100
5.2775-5.51740.28914060.217975557961100
5.5174-5.80770.27183780.218576187996100
5.8077-6.17080.26054080.212475537961100
6.1708-6.6460.24634080.219276378045100
6.646-7.31250.23284150.195775207935100
7.3125-8.36540.1874230.1775097932100
8.3654-10.51930.19423990.157375977996100
10.5193-46.47770.22793770.19987162753994

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